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1

Mutational analysis of AGXT in two Chinese families with primary hyperoxaluria type 1  

PubMed Central

Background Primary hyperoxaluria type 1 is a rare autosomal recessive disease of glyoxylate metabolism caused by a defect in the liver-specific peroxisomal enzyme alanine:glyoxylate aminotransferase (AGT) that leads to hyperoxaluria, recurrent urolithiasis, and nephrocalcinosis. Methods Two unrelated patients with recurrent urolithiasis, along with members of their families, exhibited mutations in the AGXT gene by PCR direct sequencing. Results Two heterozygous mutations that predict truncated proteins, p.S81X and p.S275delinsRAfs, were identified in one patient. The p.S81X mutation is novel. Two heterozygous missense mutations, p.M1T and p.I202N, were detected in another patient but were not identified in her sibling. These four mutations were confirmed to be of paternal and maternal origin. Conclusions These are the first cases of primary hyperoxaluria type 1 to be diagnosed by clinical manifestations and AGXT gene mutations in mainland China. The novel p.S81X and p.I202N mutations detected in our study extend the spectrum of known AGXT gene mutations.

2014-01-01

2

Primary hyperoxaluria type 1 and brachydactyly mental retardation syndrome caused by a novel mutation in AGXT and a terminal deletion of chromosome 2.  

PubMed

Primary hyperoxaluria type 1 (PH1) is an autosomal recessive disorder caused by mutations in the alanine:glyoxylate aminotransferase (AGXT) gene, located on chromosome 2q37. Mutant AGXT leads to excess production and excretion of oxalate, resulting in accumulation of calcium oxalate in the kidney, and progressive loss of renal function. Brachydactyly mental retardation syndrome (BDMR) is an autosomal dominant disorder, caused by haploinsufficiency of histone deacetylase 4 (HDAC4), also on chromosome 2q37. It is characterized by skeletal abnormalities and developmental delay. Here, we report on a girl who had phenotypes of both PH1 and BDMR. PCR-sequencing of the coding regions of AGXT showed a novel missense mutation, c.32C>G (p.Pro11Arg) inherited from her mother. Functional analyses demonstrated that it reduced the enzymatic activity to 31% of the wild-type and redirected some percentage of the enzyme away from the peroxisome. Microsatellite and array-CGH analyses indicated that the proband had a paternal de novo telomeric deletion of chromosome 2q, which included HDAC4. To our knowledge, this is the first report of PH1 and BDMR, with a novel AGXT mutation and a de novo telomeric deletion of chromosome 2q. PMID:22821680

Tammachote, Rachaneekorn; Kingsuwannapong, Nelawat; Tongkobpetch, Siraprapa; Srichomthong, Chalurmpon; Yeetong, Patra; Kingwatanakul, Pornchai; Monico, Carla G; Suphapeetiporn, Kanya; Shotelersuk, Vorasuk

2012-09-01

3

Gen IV LFR \\  

Microsoft Academic Search

This report presents the status of the model-based analysis of the publicly reported corrosion test data and use of the model to extract long term corrosion rates, a main analytical task of the LANL's Gen IV LFR Work Package \\

N. Li; J. S. Zhang; H. D. Yu; J. Jansen

4

GenBank  

PubMed Central

The GenBank nucleotide sequence database now contains sequence data and associated annotation corresponding to 85,000,000 nucleotides in 67,000 entries from a total of 3,000 organisms. The input stream of data coming into the database is primarily as direct submissions from the scientific community on electronic media, with little or no data being keyboarded from the printed page by the databank staff. The data are maintained in a relational database management system and are made available in flatfile form through on-line access, and through various network and off-line computer-readable media. The data are also distributed in relational form through satellite copies at a number of institutions in the U.S. and elsewhere. In addition, GenBank provides the U.S. distribution center for the BIOSCI electronic bulletin board service.

Burks, Christian; Cinkosky, Michael J.; Fischer, William M.; Gilna, Paul; Hayden, Jamie E.-D.; Keen, Gifford M.; Kelly, Michael; Kristofferson, David; Lawrence, Julie

1992-01-01

5

25 Years of GenBank  

MedlinePLUS

... of this page please turn Javascript on. Unique DNA database has helped advance scientific discoveries worldwide Since ... GenBank? Basically, GenBank is the biggest database of DNA in the world. Deoxyribonucleic acid (DNA) is the ...

6

Summary of CPAS Gen II Parachute Analysis  

NASA Technical Reports Server (NTRS)

The Orion spacecraft is currently under development by NASA and Lockheed Martin. Like Apollo, Orion will use a series of parachutes to slow its descent and splashdown safely. The Orion parachute system, known as the CEV Parachute Assembly System (CPAS), is being designed by NASA, the Engineering and Science Contract Group (ESCG), and Airborne Systems. The first generation (Gen I) of CPAS testing consisted of thirteen tests and was executed in the 2007-2008 timeframe. The Gen I tests provided an initial understanding of the CPAS parachutes. Knowledge gained from Gen I testing was used to plan the second generation of testing (Gen II). Gen II consisted of six tests: three singleparachute tests, designated as Main Development Tests, and three Cluster Development Tests. Gen II required a more thorough investigation into parachute performance than Gen I. Higher fidelity instrumentation, enhanced analysis methods and tools, and advanced test techniques were developed. The results of the Gen II test series are being incorporated into the CPAS design. Further testing and refinement of the design and model of parachute performance will occur during the upcoming third generation of testing (Gen III). This paper will provide an overview of the developments in CPAS analysis following the end of Gen I, including descriptions of new tools and techniques as well as overviews of the Gen II tests.

Morris, Aaron L.; Bledsoe, Kristin J.; Fraire, Usbaldo, Jr.; Moore, James W.; Olson, Leah M.; Ray, Eric

2011-01-01

7

Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend.  

PubMed

The results of a phylogenetic and chemotaxonomic analysis of the genus Micrococcus indicated that it is significantly heterogeneous. Except for Micrococcus lylae, no species groups phylogenetically with the type species of the genus, Micrococcus luteus. The other members of the genus form three separate phylogenetic lines which on the basis of chemotaxonomic properties can be assigned to four genera. These genera are the genus Kocuria gen. nov. for Micrococcus roseus, Micrococcus varians, and Micrococcus kristinae, described as Kocuria rosea comb. nov., Kocuria varians comb. nov., and Kocuria kristinae comb. nov., respectively; the genus Nesterenkonia gen. nov. for Micrococcus halobius, described as Nesterenkonia halobia comb. nov.; the genus Nesterenkonia gen. nov. for Micrococcus halobius, described as Nesterenkonia halobia comb. nov.; the genus Dermacoccus gen. nov. for Micrococcus nishinomiyaensis, described as Dermacoccus nishinomiyaensis comb. nov.; and the genus Kytocossus gen. nov. for Micrococcus sedentarius, described as Kytococcus sedentarius comb. nov. M. luteus and M. lylae, which are closely related phylogenetically but differ in some chemotaxonomic properties, are the only species that remain in the genus Micrococcus Cohn 1872. An emended description of the genus Micrococcus is given [corrected]. PMID:7547287

Stackebrandt, E; Koch, C; Gvozdiak, O; Schumann, P

1995-10-01

8

AutoGen Version 5.0  

NASA Technical Reports Server (NTRS)

Version 5.0 of the AutoGen software has been released. Previous versions, variously denoted Autogen and autogen, were reported in two articles: Automated Sequence Generation Process and Software (NPO-30746), Software Tech Briefs (Special Supplement to NASA Tech Briefs), September 2007, page 30, and Autogen Version 2.0 (NPO- 41501), NASA Tech Briefs, Vol. 31, No. 10 (October 2007), page 58. To recapitulate: AutoGen (now signifying automatic sequence generation ) automates the generation of sequences of commands in a standard format for uplink to spacecraft. AutoGen requires fewer workers than are needed for older manual sequence-generation processes, and greatly reduces sequence-generation times. The sequences are embodied in spacecraft activity sequence files (SASFs). AutoGen automates generation of SASFs by use of another previously reported program called APGEN. AutoGen encodes knowledge of different mission phases and of how the resultant commands must differ among the phases. AutoGen also provides means for customizing sequences through use of configuration files. The approach followed in developing AutoGen has involved encoding the behaviors of a system into a model and encoding algorithms for context-sensitive customizations of the modeled behaviors. This version of AutoGen addressed the MRO (Mars Reconnaissance Orbiter) primary science phase (PSP) mission phase. On previous Mars missions this phase has more commonly been referred to as mapping phase. This version addressed the unique aspects of sequencing orbital operations and specifically the mission specific adaptation of orbital operations for MRO. This version also includes capabilities for MRO s role in Mars relay support for UHF relay communications with the MER rovers and the Phoenix lander.

Gladden, Roy E.; Khanampornpan, Teerapat; Fisher, Forest W.

2010-01-01

9

Unleashing Gen Y: Marketing Mars to Millennials  

NASA Technical Reports Server (NTRS)

Space advocates need to engage Generation Y (born 1977-1999).This outreach is necessary to recruit the next generation of scientists and engineers to explore Mars. Space advocates in the non-profit, private, and government sectors need to use a combination of technical communication, marketing, and politics, to develop messages that resonate with Gen Y. Until now, space messages have been generated by and for college-educated white males; Gen Y is much more diverse, including as much as one third minorities. Young women, too, need to be reached. My research has shown that messages emphasizing technology, fun, humor, and opportunity are the best means of reaching the Gen Y audience of 60 million (US population is 300 million). The important things space advocates must avoid are talking down to this generation, making false promises, or expecting them to "wait their turn" before they can participate. This is the MTV generation! We need to find ways of engaging Gen Y now to build a future where human beings can live and work on the planet Mars. In addition to the messages themselves, advocates need to keep up with Gen Y' s social networking and use of iPods, cell phones, and the Internet. NASA and space advocacy groups can use these tools for "viral marketing," where young people share targeted space-related information via cell phones or the Internet because they like it. Overall, Gen Y is a socially dynamic and media-savvy group; advocates' space messages need to be sincere, creative, and placed in locations where Gen Y lives. Mars messages must be memorable!

Leahy, Bart D.; Hidalgo, Loretta; Kloberdanz, Cassie

2007-01-01

10

78 FR 8108 - NextGen Solutions Vendors Guide  

Federal Register 2010, 2011, 2012, 2013

...International Trade Administration NextGen Solutions Vendors Guide AGENCY: International...Air Transportation System (NextGen) solutions that meet the requirements of the International...Upgrade (ASBU) initiative. The NextGen solutions address the ICAO ASBU-designated...

2013-02-05

11

The Integrated Airport: Building a Successful NextGen Testbed  

ScienceCinema

This presentation will describe a unique public-private partnership - the Integrated Airport - that was created to engage in research and testing related to NextGen Technology deployment.  NextGen refers to the program that will be initiated to modernize the US National Airspace.  As with any major, multi-decade initiative, such as NextGen, integration of work efforts by multiple partners in the modernization is critical for success.  This talk will focus on the development of the consortium, how the consortium plans for NextGen initiatives, the series of technology demonstrations we have produced and plans for the future of NextGen testing and implementation. 

Christina Frederick-Recascino

2010-01-08

12

The Integrated Airport: Building a Successful NextGen Testbed  

SciTech Connect

This presentation will describe a unique public-private partnership - the Integrated Airport - that was created to engage in research and testing related to NextGen Technology deployment.  NextGen refers to the program that will be initiated to modernize the US National Airspace.  As with any major, multi-decade initiative, such as NextGen, integration of work efforts by multiple partners in the modernization is critical for success.  This talk will focus on the development of the consortium, how the consortium plans for NextGen initiatives, the series of technology demonstrations we have produced and plans for the future of NextGen testing and implementation. 

Christina Frederick-Recascino

2009-02-18

13

The Integrated Airport: Building a Successful NextGen Testbed  

SciTech Connect

This presentation will describe a unique public-private partnership - the Integrated Airport - that was created to engage in research and testing related to NextGen Technology deployment. NextGen refers to the program that will be initiated to modernize the US National Airspace. As with any major, multi-decade initiative, such as NextGen, integration of work efforts by multiple partners in the modernization is critical for success. This talk will focus on the development of the consortium, how the consortium plans for NextGen initiatives, the series of technology demonstrations we have produced and plans for the future of NextGen testing and implementation.

Frederick-Recascino, Christina (Embry-Riddle Aeronautical University) [Embry-Riddle Aeronautical University; Sweigard, Doug (Lockheed Martin Corporation) [Lockheed Martin Corporation; Lester, Wade (ERAU) [ERAU

2009-02-18

14

The Integrated Airport: Building a Successful NextGen Testbed  

ScienceCinema

This presentation will describe a unique public-private partnership - the Integrated Airport - that was created to engage in research and testing related to NextGen Technology deployment. NextGen refers to the program that will be initiated to modernize the US National Airspace. As with any major, multi-decade initiative, such as NextGen, integration of work efforts by multiple partners in the modernization is critical for success. This talk will focus on the development of the consortium, how the consortium plans for NextGen initiatives, the series of technology demonstrations we have produced and plans for the future of NextGen testing and implementation.

15

Gen IV Materials Handbook Implementation Plan  

SciTech Connect

A Gen IV Materials Handbook is being developed to provide an authoritative single source of highly qualified structural materials information and materials properties data for use in design and analyses of all Generation IV Reactor Systems. The Handbook will be responsive to the needs expressed by all of the principal government, national laboratory, and private company stakeholders of Gen IV Reactor Systems. The Gen IV Materials Handbook Implementation Plan provided here addresses the purpose, rationale, attributes, and benefits of the Handbook and will detail its content, format, quality assurance, applicability, and access. Structural materials, both metallic and ceramic, for all Gen IV reactor types currently supported by the Department of Energy (DOE) will be included in the Gen IV Materials Handbook. However, initial emphasis will be on materials for the Very High Temperature Reactor (VHTR). Descriptive information (e.g., chemical composition and applicable technical specifications and codes) will be provided for each material along with an extensive presentation of mechanical and physical property data including consideration of temperature, irradiation, environment, etc. effects on properties. Access to the Gen IV Materials Handbook will be internet-based with appropriate levels of control. Information and data in the Handbook will be configured to allow search by material classes, specific materials, specific information or property class, specific property, data parameters, and individual data points identified with materials parameters, test conditions, and data source. Details on all of these as well as proposed applicability and consideration of data quality classes are provided in the Implementation Plan. Website development for the Handbook is divided into six phases including (1) detailed product analysis and specification, (2) simulation and design, (3) implementation and testing, (4) product release, (5) project/product evaluation, and (6) product maintenance and enhancement. Contracting of development of the Handbook website is discussed in terms of host server options, cost, technology, developer background and cooperative nature, and company stability. One of the first and most important activities in website development will be the generation of a detailed Handbook product requirements document including case diagrams and functional requirements tables. The Implementation Plan provides a detailed overview of the organizational structure of the Handbook and details of Handbook preparation, publication, and distribution. Finally, the Implementation Plan defines Quality Assurance requirements for the Handbook.

Rittenhouse, P.; Ren, W.

2005-03-29

16

Safety Assurance in NextGen  

NASA Technical Reports Server (NTRS)

The generation of minimum operational, safety, performance, and interoperability requirements is an important aspect of safely integrating new NextGen components into the Communication Navigation Surveillance and Air Traffic Management (CNS/ATM) system. These requirements are used as part of the implementation and approval processes. In addition, they provide guidance to determine the levels of design assurance and performance that are needed for each element of the new NextGen procedures, including aircraft, operator, and Air Navigation and Service Provider. Using the enhanced Airborne Traffic Situational Awareness for InTrail Procedure (ATSA-ITP) as an example, this report describes some limitations of the current process used for generating safety requirements and levels of required design assurance. An alternative process is described, as well as the argument for why the alternative can generate more comprehensive requirements and greater safety assurance than the current approach.

HarrisonFleming, Cody; Spencer, Melissa; Leveson, Nancy; Wilkinson, Chris

2012-01-01

17

An Gen2 Based Security Authentication Protocol for RFID System  

NASA Astrophysics Data System (ADS)

EPC Class-1 Generation-2 specification(Gen2 in brief) has been accepted as the standard for RFID tags under grant number ISO18000-6C. However, Gen2 does not pay due attention to security. For this reason, a Gen2 based security authentication protocol is developed in this paper. In details, we study the security requirements presented in the current Gen2 based RFID authentication protocols[7-13]. Then we point out the security flaws of Chien's mutual authentication protocol[7], and improve the protocol based on a 11 security requirements. Our improved protocol merely uses CRC and PRNG operations supported by Gen2 and meets the 11 security requirements. In contrast to the similar work [14,15] on Chien's protocol or other Gen2 based schemes, our protocol is more secure and our security analysis is much more comprehensive and qualitative.

Yi, Xiaoluo; Wang, Liangmin; Mao, Dongmei; Zhan, Yongzhao

18

TidGen Power System Commercialization Project  

SciTech Connect

ORPC Maine, LLC, a wholly-owned subsidiary of Ocean Renewable Power Company, LLC (collectively ORPC), submits this Final Technical Report for the TidGen® Power System Commercialization Project (Project), partially funded by the U.S. Department of Energy (DE-EE0003647). The Project was built and operated in compliance with the Federal Energy Regulatory Commission (FERC) pilot project license (P-12711) and other permits and approvals needed for the Project. This report documents the methodologies, activities and results of the various phases of the Project, including design, engineering, procurement, assembly, installation, operation, licensing, environmental monitoring, retrieval, maintenance and repair. The Project represents a significant achievement for the renewable energy portfolio of the U.S. in general, and for the U.S. marine hydrokinetic (MHK) industry in particular. The stated Project goal was to advance, demonstrate and accelerate deployment and commercialization of ORPC’s tidal-current based hydrokinetic power generation system, including the energy extraction and conversion technology, associated power electronics, and interconnection equipment capable of reliably delivering electricity to the domestic power grid. ORPC achieved this goal by designing, building and operating the TidGen® Power System in 2012 and becoming the first federally licensed hydrokinetic tidal energy project to deliver electricity to a power grid under a power purchase agreement in North America. Located in Cobscook Bay between Eastport and Lubec, Maine, the TidGen® Power System was connected to the Bangor Hydro Electric utility grid at an on-shore station in North Lubec on September 13, 2012. ORPC obtained a FERC pilot project license for the Project on February 12, 2012 and the first Maine Department of Environmental Protection General Permit issued for a tidal energy project on January 31, 2012. In addition, ORPC entered into a 20-year agreement with Bangor Hydro Electric Company on January 1, 2013 for up to 5 megawatts at a price of $215/MWh, escalating at 2.0% per year.

Sauer, Christopher R. [President & CEO] [President & CEO; McEntee, Jarlath [VP Engineering & CTO] [VP Engineering & CTO

2013-12-30

19

Gen IV Materials Handbook Functionalities and Operation  

SciTech Connect

This document is prepared for navigation and operation of the Gen IV Materials Handbook, with architecture description and new user access initiation instructions. Development rationale and history of the Handbook is summarized. The major development aspects, architecture, and design principles of the Handbook are briefly introduced to provide an overview of its past evolution and future prospects. Detailed instructions are given with examples for navigating the constructed Handbook components and using the main functionalities. Procedures are provided in a step-by-step fashion for Data Upload Managers to upload reports and data files, as well as for new users to initiate Handbook access.

Ren, Weiju [ORNL

2009-12-01

20

ACE-Gen-Polymorphismus und kardiovaskuläre Erkrankungen  

Microsoft Academic Search

Zusammenfassung  Das Angiotensinkonversionsenzym (ACE) ist integraler Bestandteil der Angiotensin-II-Synthese sowie der Bradykinindegradation\\u000a und spielt somit im Metabolismus zweier vasoaktiver Peptide eine zentrale Rolle. Am Anfang dieses Jahrzehnts gelang der eindrucksvolle\\u000a Nachweis, daß das Enzym im hypertrophierten oder insuffizienten Herzen vermehrt exprimiert wird. Parallel hierzu gelang die\\u000a Charakterisierung eines Insertions\\/Deletions-(I\\/D-) Polymorphismus des humanen ACE-Gens, welcher im folgenden mit 15 bis 40%\\u000a der

Björn Mayer; Heribert Schunkert

2000-01-01

21

Back to the FutureGen?  

SciTech Connect

After years of political wrangling, Democrats may green-light the experimental clean coal power plants. The article relates how the project came to be curtailed, how Senator Dick Durbin managed to protect $134 million in funding for FutureGen in Mattoon, and how once Obama was in office a $2 billion line item to fund a 'near zero emissions power plant(s)' was placed in the Senate version of the Stimulus Bill. The final version of the legislation cut the funding to $1 billion for 'fossil energy research and development'. In December 2008 the FutureGen Alliance and the City of Mattoon spent $6.5 billion to purchase the plants eventual 440 acre site. A report by the Government Accountability Office (GAO) said that Bush's inaction may have set back clean coal technology in the US by as much as a decade. If additional funding comes through construction of the plant could start in 2010. 1 fig., 1 photo.

Buchsbaum, L.

2009-04-15

22

RxGen General Optical Model Prescription Generator  

NASA Technical Reports Server (NTRS)

RxGen is a prescription generator for JPL's in-house optical modeling software package called MACOS (Modeling and Analysis for Controlled Optical Systems), which is an expert optical analysis software package focusing on modeling optics on dynamic structures, deformable optics, and controlled optics. The objectives of RxGen are to simplify and automate MACOS prescription generations, reducing errors associated with creating such optical prescriptions, and improving user efficiency without requiring MACOS proficiency. RxGen uses MATLAB (a high-level language and interactive environment developed by MathWorks) as the development and deployment platform, but RxGen can easily be ported to another optical modeling/analysis platform. Running RxGen within the modeling environment has the huge benefit that variations in optical models can be made an integral part of the modeling state. For instance, optical prescription parameters determined as external functional dependencies, optical variations by controlling the in-/exclusion of optical components like sub-systems, and/or controlling the state of all components. Combining the mentioned capabilities and flexibilities with RxGen's optical abstraction layer completely eliminates the hindering aspects for requiring proficiency in writing/editing MACOS prescriptions, allowing users to focus on the modeling aspects of optical systems, i.e., increasing productivity and efficiency. RxGen provides significant enhancements to MACOS and delivers a framework for fast prototyping as well as for developing very complex controlled optical systems.

Sigrist, Norbert

2012-01-01

23

Head-Worn Displays for NextGen  

NASA Technical Reports Server (NTRS)

The operating concepts emerging under the Next Generation air transportation system (NextGen) require new technology and procedures - not only on the ground-side - but also on the flight deck. Flight deck display and decision support technologies are specifically targeted to overcome aircraft safety barriers that might otherwise constrain the full realization of NextGen. One such technology is the very lightweight, unobtrusive head-worn display (HWD). HWDs with an integrated head-tracking system are being researched as they offer significant potential benefit under emerging NextGen operational concepts. Two areas of benefit for NextGen are defined. First, the HWD may be designed to be equivalent to the Head-Up Display (HUD) using Virtual HUD concepts. As such, these operational credits may be provided to significantly more aircraft for which HUD installation is neither practical nor possible. Second, the HWD provides unique display capabilities, such as an unlimited field-of-regard. These capabilities may be integral to emerging NextGen operational concepts, eliminating safety issues which might otherwise constrain the full realization of NextGen. The paper details recent research results, current HWD technology limitations, and future technology development needed to realize HWDs as a enabling technology for NextGen.

Bailey, Randall E.; Shelton, Kevin J.; Arthur, J. J.

2011-01-01

24

NextGen Future Safety Assessment Game  

NASA Technical Reports Server (NTRS)

The successful implementation of the next generation infrastructure systems requires solid understanding of their technical, social, political and economic aspects along with their interactions. The lack of historical data that relate to the long-term planning of complex systems introduces unique challenges for decision makers and involved stakeholders which in turn result in unsustainable systems. Also, the need to understand the infrastructure at the societal level and capture the interaction between multiple stakeholders becomes important. This paper proposes a methodology in order to develop a holistic approach aiming to provide an alternative subject-matter expert (SME) elicitation and data collection method for future sociotechnical systems. The methodology is adapted to Next Generation Air Transportation System (NextGen) decision making environment in order to demonstrate the benefits of this holistic approach.

Ancel, Ersin; Gheorghe, Adian; Jones, Sharon Monica

2010-01-01

25

The GenDev Curriculum Development Workshop.  

PubMed

This article describes the second Curriculum Development Workshop held in May 1997 at the Asian Institute of Technology (AIT) in Bangkok, Thailand. The workshop aimed to review critically and restructure the Gender and Development Studies (GenDev) curriculum and to assess AIT's role in training gender experts for the region. Participants included 22 people from 16 countries in Asia, Europe, and the US who were teaching graduate students about gender issues and who were activists with nongovernmental organizations working on gender issues. It was determined that the following were required courses: Culture, Knowledge and Gender Relations; Gender, Technology, and Development; Principles of Gender Research and Methodology in Science and Technology; and Gender Analysis and Field Methods. Other suggested core courses included: Gender and Natural Resource Management; Enterprise Management, Technology, and Gender; Gender and Agrarian Reform; Urbanization: A Gender Perspective; Gender-Responsive Development Planning; and Gender and Economic Change: Past and Present Concerns. Participants distinguished between GenDev courses offered to anyone attending AIT and training courses designed to produce gender experts in the region. The aim of training courses for AIT graduate students was to sensitize potential managers, technologists, and others on gender issues and to create awareness of the importance of including gender perspectives within decision-making, policy formation, and implementation. Training courses to produce gender experts should be directed to those with a prior background in gender studies and include gender analysis in field methods. Participants agreed that there should be an independent and autonomous field of gender and development studies. Participants made six recommendations for such a field of study. PMID:12179927

D'cunha, J

1997-01-01

26

FutureGen Project Report, Final Technical Report.  

National Technical Information Service (NTIS)

This report summarizes the comprehensive siting, permitting, engineering, design, and costing activities completed by the FutureGen Industrial Alliance, the Department of Energy, and associated supporting subcontractors to develop a first of a kind near z...

J. Cabe M. Elliott

2010-01-01

27

1. GENERAL VIEW. Statues: Maj. Gen George Meade by Daniel ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1. GENERAL VIEW. Statues: Maj. Gen George Meade by Daniel Chester French, south side; Maj. Gen. John Reynolds by Charles Grafly, north side. Equestrian Statues: Maj. Gen George B. McClellan by Edward C. Potter, south side; Maj. Gen Winfield S. Hancock by J.Q.A. Ward, north side. The statue at the base of northern inner pedestal is Richard Smith, a type founder and donor of the Memorial. The niches are filled with eight colossal busts including Union generals, admirals, Pennsylvania governor, Memorial's architects (John T. and James H. Windrim), and executor of Smith's will. The frieze is carved with the names of eighty-four prominent Pennsylvania participants in the Civil War. - Smith Memorial Arch, Philadelphia, Philadelphia County, PA

28

EPCGen2 pseudorandom number generators: analysis of J3Gen.  

PubMed

This paper analyzes the cryptographic security of J3Gen, a promising pseudo random number generator for low-cost passive Radio Frequency Identification (RFID) tags. Although J3Gen has been shown to fulfill the randomness criteria set by the EPCglobal Gen2 standard and is intended for security applications, we describe here two cryptanalytic attacks that question its security claims: (i) a probabilistic attack based on solving linear equation systems; and (ii) a deterministic attack based on the decimation of the output sequence. Numerical results, supported by simulations, show that for the specific recommended values of the configurable parameters, a low number of intercepted output bits are enough to break J3Gen. We then make some recommendations that address these issues. PMID:24721767

Peinado, Alberto; Munilla, Jorge; Fúster-Sabater, Amparo

2014-01-01

29

EPCGen2 Pseudorandom Number Generators: Analysis of J3Gen  

PubMed Central

This paper analyzes the cryptographic security of J3Gen, a promising pseudo random number generator for low-cost passive Radio Frequency Identification (RFID) tags. Although J3Gen has been shown to fulfill the randomness criteria set by the EPCglobal Gen2 standard and is intended for security applications, we describe here two cryptanalytic attacks that question its security claims: (i) a probabilistic attack based on solving linear equation systems; and (ii) a deterministic attack based on the decimation of the output sequence. Numerical results, supported by simulations, show that for the specific recommended values of the configurable parameters, a low number of intercepted output bits are enough to break J3Gen. We then make some recommendations that address these issues.

Peinado, Alberto; Munilla, Jorge; Fuster-Sabater, Amparo

2014-01-01

30

GenMAPP and MAPPFinder for Systems Biology Education  

NSDL National Science Digital Library

The GenMAPP and MAPPFinder system provides a framework for learning about the properties of biochemical and gene regulatory pathways. Students can research a pathway in conjunction with a course topic and then draw it out with the GenMAPP graphics tools. Students can then color-code the pathway with publicly available microarray data, connecting them to cutting-edge research. The pathways the students draw can be submitted to the public pathway repository at www.GenMAPP.org, their work making a contribution to practicing scientists. In summary, the systems level approach provided by GenMAPP moves seamlessly from class projects to independent research and will allow students to make a contribution to the scientific community.

Kam Dahlquist (Loyola Marymount University;)

2004-06-12

31

Sources of data in the GenBank database  

SciTech Connect

The citations in GenBank are characterized with respect to form of publication. The potential spectrum of quality control problems applicable to the various types of unpublished data are discussed. 6 refs., 2 tabs.

Burks, C.

1987-01-01

32

98. SWITCH HOUSE MAIN LOBBY, GEN 3 CIRCUIT BREAKER, VIEW ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

98. SWITCH HOUSE MAIN LOBBY, GEN 3 CIRCUIT BREAKER, VIEW OF OPPOSITE SIDE FROM HAER No. PA-505-97 - Delaware County Electric Company, Chester Station, Delaware River at South end of Ward Street, Chester, Delaware County, PA

33

JEqualityGen: generating equality and hashing methods  

Microsoft Academic Search

Manually implementing equals (for object comparisons) and hashCode (for object hashing) methods in large software projects is tedious and error-prone. This is due to many special cases, such as field shadowing, comparison between different types, or cyclic object graphs. Here, we present JEqualityGen, a source code generator that automatically derives implementations of these methods. JEqualityGen proceeds in two states: it

Neville Grech; Julian Rathke; Bernd Fischer

2011-01-01

34

SEQ-GEN: A comprehensive multimission sequencing system  

NASA Technical Reports Server (NTRS)

SEQ-GEN is a user-interactive computer program used to plan and generate a sequence of commands for spacecraft. Desired activities are specified by the user of SEQ-GEN; SEQ-GEN in turn expands these activities, deriving the spacecraft commands necessary to accomplish the desired activities. SEQ-GEN models the effects on the spacecraft of the commands, predicting the state as a function of time, flagging any conflicts and rule violations. These states, conflicts, and violations are viewable both graphically and textually at the user's request. SEQ-GEN also displays the entire sequence graphically, showing each requested activity as a bar on its graphical timeline. SEQ-GEN immediately revalidates the sequence, updating its models and calculations along with its displays based on these changes. Because it has the ability to recalculate spacecraft states immediately, the user is able to perform 'what-if' sessions easily. SEQ-GEN, a multimission tool, is adaptable to any flight project. A flight project writes its adaptation files containing project unique information including in its simplest form, only spacecraft commands. For more involved projects the adaptation files may also contain flight and mission rules, description of the spacecraft and ground models, and the definition of activities. SEQ-GEN operates at whatever level of detail the adaptation files imply. Simple adaptations are straight forward to do. There is, however, no limit to the complexity of activity definitions or of spacecraft models: both may involve unlimited logical decision points. Commands and activities may involve any number of parameters of a wide variety of data types, including integer, float, time, boolean, and character strings. SEQ-GEN will be used by the Mars Pathfinder, Cassini, and VIM (Voyager Interstellar Mission) project in an effort to speed up adaptation time and to keep sequence generation costs down. SEQ-GEN is hosted on UNIX workstations. It uses MOTIF and X for windowing, and was designed and coded in an object-oriented style in the language C++.

Salcedo, Jose; Starbird, Thomas J.

1994-01-01

35

76 FR 28973 - Terra-Gen Dixie Valley, LLC; Order on Rehearing and Accepting Tariff Filing, Subject to...  

Federal Register 2010, 2011, 2012, 2013

...matters in the following sections. a. Clustering and Effective Date i. Terra-Gen Tariff...Terra-Gen proposes provisions to address clustering of transmission system impact studies...studies.\\22\\ Terra-Gen's proposed clustering provisions provide, among other...

2011-05-19

36

A Novel Role of Human Holliday Junction Resolvase GEN1 in the Maintenance of Centrosome Integrity  

PubMed Central

The maintenance of genomic stability requires accurate genome replication, repair of DNA damage, and the precise segregation of chromosomes in mitosis. GEN1 possesses Holliday junction resolvase activity in vitro and presumably functions in homology driven repair of DNA double strand breaks. However, little is currently known about the cellular functions of human GEN1. In the present study we demonstrate that GEN1 is a novel centrosome associated protein and we characterize the various phenotypes associated with GEN1 deficiency. We identify an N-terminal centrosome localization signal in GEN1, which is required and sufficient for centrosome localization. We report that GEN1 depletion results in aberrant centrosome numbers associated with the formation of multiple spindle poles in mitosis, an increased number of cells with multi-nuclei, increased apoptosis and an elevated level of spontaneous DNA damage. We find homologous recombination severely impaired in GEN1 deficient cells, suggesting that GEN1 functions as a Holliday junction resolvase in vivo as well as in vitro. Complementation of GEN1 depleted cells with various GEN1 constructs revealed that centrosome association but not catalytic activity of GEN1 is required for preventing centrosome hyper-amplification, formation of multiple mitotic spindles, and multi-nucleation. Our findings provide novel insight into the biological functions of GEN1 by uncovering an important role of GEN1 in the regulation of centrosome integrity.

Zhou, Dong-Ping; Xu, Qian; Li, Miao-Miao; Wang, Zhao-Qi; Tong, Wei-Min; Yang, Yun-Gui

2012-01-01

37

VirGen: a comprehensive viral genome resource  

PubMed Central

VirGen is a comprehensive viral genome resource that organizes the ‘sequence space’ of viral genomes in a structured fashion. It has been developed with the objective of serving as an annotated and curated database comprising complete genome sequences of viruses, value-added derived data and data mining tools. The current release (v1.1) contains 559 complete genomes in addition to 287 putative genomes of viruses belonging to eight viral families for which the host range includes animals and plants. Viral genomes in VirGen are annotated using sequence-based Bioinformatics approaches. The genomic data is also curated to identify ‘alternate names’ of viral proteins, where available. VirGen archives the results of comparisons of genomes, proteomes and individual proteins within and between viral species. It is the first resource to provide phylogenetic trees of viral species computed using whole-genome sequence data. The module of predicted B-cell antigenic determinants in VirGen is an attempt to link the genome to its vaccinome. Comparative genome analysis data facilitate the study of genome organization and evolution of viruses, which would have implications in applied research to identify candidates for the design of vaccines and antiviral drugs. VirGen is a relational database and is available at http://bioinfo.ernet.in/virgen/virgen.html.

Kulkarni-Kale, Urmila; Bhosle, Shriram; Manjari, G. Sunitha; Kolaskar, A. S.

2004-01-01

38

Training trust in automation within a NextGen environment  

NASA Astrophysics Data System (ADS)

The projected increase in air traffic density has led to the development of NextGen that is expected to revolutionize the way the NAS is currently functioning. For NextGen to be implemented successfully, it is important to understand the humanautomation relationship within a complex system. Controllers will have to rely on automated tools to successfully manage aircraft in their sector. Increasing human trust in automation can lead to an increase in automation acceptance and its proper use. However, we are not aware of any research studies that have attempted to directly train individuals to trust automation. We report on an attempt to train 8 novice air traffic controllers to trust the automated NextGen tools in a radar internship course. Although the results were not statistically significant, the trend in the data suggests that it may be possible to train trust in automation.

Higham, Tiana-Lynn M.

39

Fossil energy, clean coal technology, and FutureGen  

SciTech Connect

Future fossil use will rely heavily on carbon sequestration. Clean coal technologies are being incorporated in the USA, including air pollution control, and will need to incorporate carbon capture and sequestration. The paper ends with an outline of the restructured FutureGen project. 7 figs.

Sarkus, T.A.

2008-07-15

40

A New Parent Generation: Meet Mr. and Mrs. Gen X  

ERIC Educational Resources Information Center

Slowly but surely, Generation Xers have been taking over from Baby Boomers as the majority of parents in elementary and secondary education. Gen-X parents and Boomer parents belong to two neighboring generations, each possessing its own location in history and its own peer personality. They are similar in some respects, but clearly different in…

Howe, Neil

2010-01-01

41

Meet Mr. and Mrs. Gen X: A New Parent Generation  

ERIC Educational Resources Information Center

Slowly but surely, Generation Xers have been taking over from Baby Boomers as the majority of parents in elementary and secondary education. In the early 1990s, Gen Xers began joining parent-teacher associations in the nation's elementary schools. Around 2005, they became the majority of middle school parents. By the fall of 2008, they took over…

Howe, Neil

2010-01-01

42

Biogas Purification Process to Increase Gen-Set Efficiency  

NASA Astrophysics Data System (ADS)

Because of global issue about limited energy, biogas was one of alternative energy and save energy in the world which produced from biomass especially from cow manure. Most of biogas which produced from cow manure contains 40-75% methane as energy resources and another gas as impurities. Methane concentration of biogas has relation with biogas energy value, especially for application as fuel of electricity conversion using gen-set. For increasing gen-set efficiency can be held by increasing methane concentration of biogas using biogas purification process. Biogas purification process can be held by adsorption system which using activated zeolite as absorber. After biogas through the purification system, methane concentration was increasing and impacting to gen-set efficiency especially voltage value was increasing until 22 times in average better than without purification and keeping power stability, so it will produce electricity conversion until 39,07% of practical and 38,09% of equation calculation from maximum electric power output of gen-set.

Krido Wahono, Satriyo; Maryana, Roni; Kismurtono, M.

2009-09-01

43

An electronic flight bag for NextGen avionics  

NASA Astrophysics Data System (ADS)

The introduction of the Next Generation Air Transportation System (NextGen) initiative by the Federal Aviation Administration (FAA) will impose new requirements for cockpit avionics. A similar program is also taking place in Europe by the European Organisation for the Safety of Air Navigation (Eurocontrol) called the Single European Sky Air Traffic Management Research (SESAR) initiative. NextGen will require aircraft to utilize Automatic Dependent Surveillance-Broadcast (ADS-B) in/out technology, requiring substantial changes to existing cockpit display systems. There are two ways that aircraft operators can upgrade their aircraft in order to utilize ADS-B technology. The first is to replace existing primary flight displays with new displays that are ADS-B compatible. The second, less costly approach is to install an advanced Class 3 Electronic Flight Bag (EFB) system. The installation of Class 3 EFBs in the cockpit will allow aircraft operators to utilize ADS-B technology in a lesser amount of time with a decreased cost of implementation and will provide additional benefits to the operator. This paper describes a Class 3 EFB, the NexisTM Flight-Intelligence System, which has been designed to allow users a direct interface with NextGen avionics sensors while additionally providing the pilot with all the necessary information to meet NextGen requirements.

Zelazo, D. Eyton

2012-05-01

44

GEN-SYSTEM - A new experimental philosophy for EISCAT radars  

Microsoft Academic Search

GEN-SYSTEM is a code name for a new experimental design philosphy, a set of related correlator algorithms and an experiment library based on this philosophy. It is designed to obtain an easy way to develop powerful experiments having several different modulations in the same pattern or to have very powerful modulations in single channel experiments, needed sometimes in special applications.

Tauno Turunen

1986-01-01

45

DOE/NNSA perspective safeguard by design: GEN III/III+ light water reactors and beyond  

SciTech Connect

An overview of key issues relevant to safeguards by design (SBD) for GEN III/IV nuclear reactors is provided. Lessons learned from construction of typical GEN III+ water reactors with respect to SBD are highlighted. Details of SBD for safeguards guidance development for GEN III/III+ light water reactors are developed and reported. This paper also identifies technical challenges to extend SBD including proliferation resistance methodologies to other GEN III/III+ reactors (except HWRs) and GEN IV reactors because of their immaturity in designs.

Pan, Paul Y [Los Alamos National Laboratory

2010-12-10

46

Advanced Vehicle Concepts and Implications for NextGen  

NASA Technical Reports Server (NTRS)

This report presents the results of a major NASA study of advanced vehicle concepts and their implications for the Next Generation Air Transportation System (NextGen). Comprising the efforts of dozens of researchers at multiple institutions, the analyses presented here cover a broad range of topics including business-case development, vehicle design, avionics, procedure design, delay, safety, environmental impacts, and metrics. The study focuses on the following five new vehicle types: Cruise-efficient short takeoff and landing (CESTOL) vehicles Large commercial tiltrotor aircraft (LCTRs) Unmanned aircraft systems (UAS) Very light jets (VLJs) Supersonic transports (SST). The timeframe of the study spans the years 2025-2040, although some analyses are also presented for a 3X scenario that has roughly three times the number of flights as today. Full implementation of NextGen is assumed.

Blake, Matt; Smith, Jim; Wright, Ken; Mediavilla Ricky; Kirby, Michelle; Pfaender, Holger; Clarke, John-Paul; Volovoi, Vitali; Dorbian, Christopher; Ashok, Akshay; Reynolds, Tom; Waitz, Ian; Hileman, James; Arunachalam, Sarav; Hedrick, Matt; Vempati, Lakshmi; Laroza, Ryan; denBraven, Wim; Henderson, Jeff

2010-01-01

47

Crossiella gen. nov., a new genus related to Streptoalloteichus.  

PubMed

Phylogenetic analysis of the genera within the suborder Pseudonocardineae based on almost complete sequences of 16S rDNA showed that Saccharothrix cryophilis NRRL B-16238T was misplaced within the genus Saccharothrix. Saccharothrix cryophilis NRRL B-16238T appeared to be phylogenetically closest to Streptoalloteichus, but is morphologically distinct from this genus because sporangia with motile spores are not observed. The aerial mycelium fragments into rod-shaped elements and sclerotium-like bodies are observed occasionally in the substrate mycelium. The cell wall contains meso-diaminopimelic acid, whole-cell hydrolysates contain galactose, rhamnose and ribose, the phospholipid pattern is type PIV and the principal menaquinone is MK-9(H4). A new genus to accommodate Saccharothrix cryophilis is proposed, Crossiella gen. nov., in recognition of the contributions of Thomas Cross, a distinguished actinomycete biologist at the University of Bradford, UK. The type species is Crossiella cryophila gen. nov., comb. nov. PMID:11491360

Labeda, D P

2001-07-01

48

Virally Inspired: Gen Y Perceptions of Viral Stealth Marketing  

Microsoft Academic Search

Viral stealth marketing is electronic promotions presented as word-of-mouth communication. People spreading these messages conceal the fact that they are paid to promote a product. Non-disclosure raises important ethical questions, as well as the practical problem of the consequences of being found out. Two surveys were uploaded to social networking sites, targeted at Gen Y, with one depicting a viral-marketing

Hume Winzar; Celeste Swanepoel; Ashley Lye

49

Kankakeea gen. nov., buds for vegetative reproduction in Carboniferous ferns  

Microsoft Academic Search

Summary  \\u000a Kankakeea gen. nov. is a lobed thalloid structure that commonly is dichotomous. It grows at the tip of a pinna or frond rachis and\\u000a can be shed.Kankakeea is interpreted as being a bud for vegetative propagation in ferns. It is known from the Pennsylvanian of Illinois and Upper\\u000a Carboniferous of France.

Hermann W. Pfefferkorn

1973-01-01

50

Mutation des menschlichen hairless-Gens bei Atrichia universalis  

Microsoft Academic Search

Zusammenfassung  \\u000a Unlängst wurde in einer pakistanischen Sippe mit einer autosomal-rezessiven Form der kongenitalen universellen Atrichie eine\\u000a Mutation des humanen Homologs zum Maus-hairless-Gen auf Chromosom 8p12 identifiziert. Unter den verschiedenen Formen des hereditären Haarverlustes bei Menschen repräsentiert\\u000a die Atrichia universalis eine seltene Entität, die nichts mit den häufigsten Ursachen von Haarverlust zu tun hat, nämlich\\u000a androgenetische Alopezia (AGA) und Alopecia areata

Ralph M. Trüeb

1998-01-01

51

Downscaling extremes with EDS, TreeGen, and BCSD  

NASA Astrophysics Data System (ADS)

We conduct an intercomparison of the ability of three statistical downscaling methods, Expanded Downscaling (EDS), TreeGen, and the Bias-Corrected Spatial Disaggregation (BCSD) scheme, to represent the statistics of climatic extremes. These three methods represent fairly different approaches to the downscaling problem: EDS is based on regression, TreeGen uses synoptic weather types, and BCSD combines quantile mapping and resampling. EDS and TreeGen are driven by daily atmospheric predictor fields and therefore allow for the verification of single extreme events using daily analysis fields (ECMWF, NCEP) and station data. BCSD is driven by monthly fields, while daily data are generated semi-stochastically by resampling the historical record. BCSD simulated events are therefore not directly comparable to observed ones. Long-term statistics are, however, so we compare appropriate measures for local extremes from all three methods, using an independent analysis period. Extreme event statistics are taken from ClimDex, a set of impact-oriented indices derived from the STARDEX project. The downscaling will be applied to several areas in British Columbia that are representative of the provinces' major climatic zones. The resulting methodological uncertainty will be assessed against the natural uncertainty stemming from different realizations of the present climate, as downscaled from analyses or from simulations forced by present-day greenhouse gas concentrations (20C3M) using three different climate models.

Buerger, G.; Murdock, T.; Werner, A. T.

2010-12-01

52

J3Gen: A PRNG for Low-Cost Passive RFID  

PubMed Central

Pseudorandom number generation (PRNG) is the main security tool in low-cost passive radio-frequency identification (RFID) technologies, such as EPC Gen2. We present a lightweight PRNG design for low-cost passive RFID tags, named J3Gen. J3Gen is based on a linear feedback shift register (LFSR) configured with multiple feedback polynomials. The polynomials are alternated during the generation of sequences via a physical source of randomness. J3Gen successfully handles the inherent linearity of LFSR based PRNGs and satisfies the statistical requirements imposed by the EPC Gen2 standard. A hardware implementation of J3Gen is presented and evaluated with regard to different design parameters, defining the key-equivalence security and nonlinearity of the design. The results of a SPICE simulation confirm the power-consumption suitability of the proposal.

Melia-Segui, Joan; Garcia-Alfaro, Joaquin; Herrera-Joancomarti, Jordi

2013-01-01

53

J3Gen: a PRNG for low-cost passive RFID.  

PubMed

Pseudorandom number generation (PRNG) is the main security tool in low-cost passive radio-frequency identification (RFID) technologies, such as EPC Gen2. We present a lightweight PRNG design for low-cost passive RFID tags, named J3Gen. J3Gen is based on a linear feedback shift register (LFSR) configured with multiple feedback polynomials. The polynomials are alternated during the generation of sequences via a physical source of randomness. J3Gen successfully handles the inherent linearity of LFSR based PRNGs and satisfies the statistical requirements imposed by the EPC Gen2 standard. A hardware implementation of J3Gen is presented and evaluated with regard to different design parameters, defining the key-equivalence security and nonlinearity of the design. The results of a SPICE simulation confirm the power-consumption suitability of the proposal. PMID:23519344

Melià-Seguí, Joan; Garcia-Alfaro, Joaquin; Herrera-Joancomartí, Jordi

2013-01-01

54

GenEd - An Editor with Generic Semantics for Formal Reasoning about Visual Notations  

Microsoft Academic Search

We describe the object-oriented editor GenEd support- ing the design of specifications for visual notations. Prominent features of GenEd are (1) it is generic, i.e. domain-specific syntax and semantics are specified by users; (2) built-in parser for actual drawings, driven by formal specifications; (3) powerful reasoning capabili- ties about diagrams and their specification. GenEd's specification language is based on a

Volker Haarslev; Michael Wessel

1996-01-01

55

76 FR 22162 - Third Meeting RTCA NextGen Advisory Committee (NAC)  

Federal Register 2010, 2011, 2012, 2013

...Association. Break. Review Recommendations to... Lunch Break. Review Recommendations to...Integrated Capabilities Scoping and Requirements. Review Recommendations to...NextGen Measurement Methodology. Review...

2011-04-20

56

GRAIL and GenQuest Sequence Annotation Tools  

SciTech Connect

Our goal is to develop and implement an integrated intelligent system which can recognize biologically significant features in DNA sequence and provide insight into the organization and function of regions of genomic DNA. GRAIL is a modular expert system which facilitates the recognition of gene features and provides an environment for the construction of sequence annotation. The last several years have seen a rapid evolution of the technology for analyzing genomic DNA sequences. The current GRAIL systems (including the e-mail, XGRAIL, JAVA-GRAIL and genQuest systems) are perhaps the most widely used, comprehensive, and user friendly systems available for computational characterization of genomic DNA sequence.

Xu, Ying; Shah, Manesh B.; Einstein, J. Ralph; Parang, Morey; Snoddy, Jay; Petrov, Sergey; Olman, Victor; Zhang, Ge; Mural, Richard J.; Uberbacher, Edward C.

1997-12-31

57

Simplified dynamic density: A metric for dynamic airspace configuration and NextGen analysis  

Microsoft Academic Search

The next generation air transportation system (NextGen) is expected to bring about major improvements in both airspace design and utilization. One element of NextGen, dynamic airspace configuration (DAC), is proposed as a means to facilitate substantially more efficient airspace capacity management. A new metric or set of metrics is required for analyzing future airspace design concepts like DAC. These metrics

Alexander Klein; Mark D. Rodgers; K. Leiden

2009-01-01

58

Polkepsilonema mombasae gen. et sp.n. and Pternepsilonema servaesae gen. et sp.n. (Nematoda, Epsilonematidae) from East African coasts  

Microsoft Academic Search

Two new genera and species from Kenyan tidal areas,Polkepsilonema mombasae gen. et sp.n. andPternepsilonema servaesae gen. et sp.n., are described. Both are characterized by the presence of at least fourteen subcephalic setae and by thick thorns on the ventral body region of males. In the first genus, eight to ten subcephalic setae are situated anterior to the amphid, and the

Dominick Verschelde; Magda Vincx

1993-01-01

59

GenGIS: A geospatial information system for genomic data  

PubMed Central

The increasing availability of genetic sequence data associated with explicit geographic and ecological information is offering new opportunities to study the processes that shape biodiversity. The generation and testing of hypotheses using these data sets requires effective tools for mathematical and visual analysis that can integrate digital maps, ecological data, and large genetic, genomic, or metagenomic data sets. GenGIS is a free and open-source software package that supports the integration of digital map data with genetic sequences and environmental information from multiple sample sites. Essential bioinformatic and statistical tools are integrated into the software, allowing the user a wide range of analysis options for their sequence data. Data visualizations are combined with the cartographic display to yield a clear view of the relationship between geography and genomic diversity, with a particular focus on the hierarchical clustering of sites based on their similarity or phylogenetic proximity. Here we outline the features of GenGIS and demonstrate its application to georeferenced microbial metagenomic, HIV-1, and human mitochondrial DNA data sets.

Parks, Donovan H.; Porter, Michael; Churcher, Sylvia; Wang, Suwen; Blouin, Christian; Whalley, Jacqueline; Brooks, Stephen; Beiko, Robert G.

2009-01-01

60

Genetic code prediction for metazoan mitochondria with GenDecoder.  

PubMed

There is a standard genetic code that is used by most organisms, but exceptions exist in which particular codons are translated with a different meaning, i.e., as a different amino acid. The characterization of the genetic code of an organism is hence a key step for properly analyzing and translating its protein-coding genes. Such characterization is particularly important in the case of metazoan mitochondrial genomes for two reasons: first, many variant codes occur in them and second, mitochondrial data is frequently used for evolutionary studies. Variant codes are usually found by comparative sequence analyses. Given a protein alignment, if a particular codon for a given species occurs at positions in which a particular amino acid is frequently found in other species, then the most likely hypothesis is that the codon is translated as that particular amino acid in that species. Previously, we have shown that this method can be very reliable provided that enough taxa and positions are included in the comparisons and have implemented it in the web-ser GenDecoder (http://darwin.uvigo.es/software/gendecoder.html). In this chapter we describe the rationale of the method used by GenDecoder and its usage through worked examples, highlighting the potential problems that can arise during the analysis. PMID:19378147

Abascal, Federico; Zardoya, Rafael; Posada, David

2009-01-01

61

Influence of tidal parameters on SeaGen flicker performance.  

PubMed

This paper presents the analysis of the study of the flicker emitted from the 1.2?MW tidal energy converter (TEC), SeaGen, against varying tidal parameters. This paper outlines the main elements of the TEC itself, the environment it is located in and the measurement set up. In this paper, the flicker emitted by the TEC is compared with the different tidal parameters, including flood and ebb tides, tidal speed, water depth and turbulence strength and intensity. Flicker emissions have been calculated from measured data in over 90 measurement (10?min) periods, and all of the tidal parameters vary significantly over that testing period. This allows for a detailed statistical and graphical analysis of the variation of flicker with the variation of the tidal parameters outlined above. It is found, with the exception of tidal speed, that there is no strong relationship between flicker emissions and any other tidal parameter. As SeaGen is an asymmetrical TEC with full blade pitching for flood and ebb generation, it was also found that the expected difference of flicker emissions owing to the effect of the submersed crossbeam was not significant. The TEC harmonic performance versus tidal speed is also presented. PMID:23319709

MacEnri, Joseph; Reed, Matthew; Thiringer, Torbjörn

2013-02-28

62

Next gen wavelets down-sampling preserving statistics  

NASA Astrophysics Data System (ADS)

We extend the 2nd Gen Discrete Wavelet Transform (DWT) of Swelden to the Next Generations (NG) Digital Wavelet Transform (DWT) preserving the statistical salient features. The lossless NG DWT accomplishes the data compression of "wellness baseline profiles (WBP)" of aging population at homes. For medical monitoring system at home fronts we translate the military experience to dual usage of veterans & civilian alike with the following three requirements: (i) Data Compression: The necessary down sampling reduces the immense amount of data of individual WBP from hours to days and to weeks for primary caretakers in terms of moments, e.g. mean value, variance, etc., without the artifacts caused by FFT arbitrary windowing. (ii) Lossless: our new NG_DWT must preserve the original data sets. (iii) Phase Transition: NG_DWT must capture the critical phase transition of the wellness toward the sickness with simultaneous display of local statistical moments. According to the Nyquist sampling theory, assuming a band-limited wellness physiology, we must sample the WBP at least twice per day since it is changing diurnally and seasonally. Since NG_DWT, like the 2nd Gen, is lossless, we can reconstruct the original time series for the physicians' second looks. This technique of NG_DWT can also help stock market day-traders monitoring the volatility of multiple portfolios without artificial horizon artifacts.

Szu, Harold; Miao, Lidan; Chanyagon, Pornchai; Cader, Masud

2007-04-01

63

Goodfellowia gen. nov., a new genus of the Pseudonocardineae related to Actinoalloteichus, containing Goodfellowia coeruleoviolacea gen. nov., comb. nov.  

PubMed

During the course of a phylogenetic evaluation of Saccharothrix strains held in the ARS Culture Collection, it was discovered that Saccharothrix coeruleoviolacea NRRL B-24058(T) is unrelated to other species within this genus, and a polyphasic study was undertaken to clarify its taxonomic position. Strain NRRL B-24058(T) is observed to be phylogenetically separate from the genus Saccharothrix and is most closely related to the genus Actinoalloteichus. The strain exhibits chemotaxonomic properties that distinguish it from members of Actinoalloteichus, including a whole-cell sugar pattern consisting of galactose and ribose as diagnostic sugars, phosphatidylethanolamine, phosphatidylethanolamine containing 2-OH fatty acids and diphosphatidylglycerol as the predominant polar lipids and MK-9(H(4)) and MK-10(H(4)) as the only menaquinones observed. Strain NRRL B-24058(T) is distinct from other taxa within the suborder Pseudonocardineae and a new genus to be named Goodfellowia gen. nov. is proposed. The type species of this new genus is Goodfellowia coeruleoviolacea gen. nov., comb. nov., and the type strain is NRRL B-24058(T) (=DSM 43935(T) = INA 3564(T) = JCM 9110(T) = NBRC 14988(T) = VKM Ac-1083(T)). PMID:16738092

Labeda, D P; Kroppenstedt, R M

2006-06-01

64

Hand-held optical imager (Gen-2): improved instrumentation and target detectability  

PubMed Central

Abstract. Hand-held optical imagers are developed by various researchers towards reflectance-based spectroscopic imaging of breast cancer. Recently, a Gen-1 handheld optical imager was developed with capabilities to perform two-dimensional (2-D) spectroscopic as well as three-dimensional (3-D) tomographic imaging studies. However, the imager was bulky with poor surface contact (?30%) along curved tissues, and limited sensitivity to detect targets consistently. Herein, a Gen-2 hand-held optical imager that overcame the above limitations of the Gen-1 imager has been developed and the instrumentation described. The Gen-2 hand-held imager is less bulky, portable, and has improved surface contact (?86%) on curved tissues. Additionally, the forked probe head design is capable of simultaneous bilateral reflectance imaging of both breast tissues, and also transillumination imaging of a single breast tissue. Experimental studies were performed on tissue phantoms to demonstrate the improved sensitivity in detecting targets using the Gen-2 imager. The improved instrumentation of the Gen-2 imager allowed detection of targets independent of their location with respect to the illumination points, unlike in Gen-1 imager. The developed imager has potential for future clinical breast imaging with enhanced sensitivity, via both reflectance and transillumination imaging.

Gonzalez, Jean; DeCerce, Joseph; Erickson, Sarah J.; Martinez, Sergio L.; Nunez, Annie; Roman, Manuela; Traub, Barbara; Flores, Cecilia A.; Roberts, Seigbeh M.; Hernandez, Estrella; Aguirre, Wenceslao; Kiszonas, Richard; Godavarty, Anuradha

2012-01-01

65

Hand-held optical imager (Gen-2): improved instrumentation and target detectability  

NASA Astrophysics Data System (ADS)

Hand-held optical imagers are developed by various researchers towards reflectance-based spectroscopic imaging of breast cancer. Recently, a Gen-1 handheld optical imager was developed with capabilities to perform two-dimensional (2-D) spectroscopic as well as three-dimensional (3-D) tomographic imaging studies. However, the imager was bulky with poor surface contact (˜30%) along curved tissues, and limited sensitivity to detect targets consistently. Herein, a Gen-2 hand-held optical imager that overcame the above limitations of the Gen-1 imager has been developed and the instrumentation described. The Gen-2 hand-held imager is less bulky, portable, and has improved surface contact (˜86%) on curved tissues. Additionally, the forked probe head design is capable of simultaneous bilateral reflectance imaging of both breast tissues, and also transillumination imaging of a single breast tissue. Experimental studies were performed on tissue phantoms to demonstrate the improved sensitivity in detecting targets using the Gen-2 imager. The improved instrumentation of the Gen-2 imager allowed detection of targets independent of their location with respect to the illumination points, unlike in Gen-1 imager. The developed imager has potential for future clinical breast imaging with enhanced sensitivity, via both reflectance and transillumination imaging.

Gonzalez, Jean; DeCerce, Joseph; Erickson, Sarah J.; Martinez, Sergio L.; Nunez, Annie; Roman, Manuela; Traub, Barbara; Flores, Cecilia A.; Roberts, Seigbeh M.; Hernandez, Estrella; Aguirre, Wenceslao; Kiszonas, Richard; Godavarty, Anuradha

2012-08-01

66

Mutation and association analysis of GEN1 in breast cancer susceptibility.  

PubMed

GEN1 was recently identified as a key Holliday junction resolvase involved in homologous recombination. Somatic truncating GEN1 mutations have been reported in two breast cancers. Together these data led to the proposition that GEN1 is a breast cancer predisposition gene. In this article we have formally investigated this hypothesis. We performed full-gene mutational analysis of GEN1 in 176 BRCA1/2-negative familial breast cancer samples and 159 controls. We genotyped six SNPs tagging the 30 common variants in the transcribed region of GEN1 in 3,750 breast cancer cases and 4,907 controls. Mutation analysis revealed one truncating variant, c.2515_2519delAAGTT, which was present in 4% of cases and 4% of controls. We identified control individuals homozygous for the deletion, demonstrating that the last 69 amino acids of GEN1 are dispensable for its function. We identified 17 other variants, but their frequency did not significantly differ between cases and controls. Analysis of 3,750 breast cancer cases and 4,907 controls demonstrated no evidence of significant association with breast cancer for six SNPs tagging the 30 common GEN1 variants. These data indicate that although it also plays a key role in double-strand DNA break repair, GEN1 does not make an appreciable contribution to breast cancer susceptibility by acting as a high- or intermediate-penetrance breast cancer predisposition gene like BRCA1, BRCA2, CHEK2, ATM, BRIP1 and PALB2 and that common GEN1 variants do not act as low-penetrance susceptibility alleles analogous to SNPs in FGFR2. Furthermore, our analyses demonstrate the importance of undertaking appropriate genetic investigations, typically full gene screening in cases and controls together with large-scale case-control association analyses, to evaluate the contribution of genes to cancer susceptibility. PMID:20512659

Turnbull, Clare; Hines, Sarah; Renwick, Anthony; Hughes, Deborah; Pernet, David; Elliott, Anna; Seal, Sheila; Warren-Perry, Margaret; Gareth Evans, D; Eccles, Diana; Stratton, Michael R; Rahman, Nazneen

2010-11-01

67

The Madagascan endemic myrmicine ants related to Eutetramorium (Hymenoptera: Formicidae): taxonomy of the genera Eutetramorium Emery, Malagidris nom. n., Myrmisaraka gen. n., Royidris gen. n., and Vitsika gen. n.  

PubMed

The monophyletic group of myrmicine ant genera related to Eutetramorium is described and its taxonomy is documented. The group is endemic in Madagascar and contains five genera: Eutetramorium Emery, 1899 (3 species, 1 of which is new); Malagidris nom. n., a replacement name for Brunella Forel, 1917, junior homonym of Brunella Smith, G.W. 1909 (Crustacea) (6 species, 5 of which are new); Myrmisaraka gen. n. (2 species, both new); Royidris gen. n. (15 species, 11 of which are new); Vitsika gen. n. (14 species, all of which are new). Keys to the worker caste are provided for all genera, and provisional keys to known males are given for Malagidris and Vitsika. PMID:24869996

Bolton, Barry; Fisher, Brian L

2014-01-01

68

Ferrimicrobium acidiphilum gen. nov., sp. nov. and Ferrithrix thermotolerans gen. nov., sp. nov.: heterotrophic, iron-oxidizing, extremely acidophilic actinobacteria.  

PubMed

Two novel extremely acidophilic, iron-oxidizing actinobacteria were isolated, one from a mine site in North Wales, UK (isolate T23(T)), and the other from a geothermal site in Yellowstone National Park, Wyoming, USA (Y005(T)). These new actinobacteria belong to the subclass Acidimicrobidae, and in contrast to the only other classified member of the subclass (Acidimicrobium ferrooxidans), both isolates were obligate heterotrophs. The mine site isolate was mesophilic and grew as small rods, while the Yellowstone isolate was a moderate thermophile and grew as long filaments, forming macroscopic flocs in liquid media. Both isolates accelerated the oxidative dissolution of pyrite in yeast extract-amended cultures, but neither was able to oxidize reduced forms of sulfur. Ferrous iron oxidation enhanced growth yields of the novel mesophilic actinobacterium T23(T), though this was not confirmed for the Yellowstone isolate. Both isolates catalysed the dissimilatory reduction of ferric iron, using glycerol as electron donor, in oxygen-free medium. Based on comparative analyses of base compositions of their chromosomal DNA and of their 16S rRNA gene sequences, the isolates are both distinct from each other and from Acidimicrobium ferrooxidans, and are representatives of two novel genera. The names Ferrimicrobium acidiphilum gen. nov., sp. nov. and Ferrithrix thermotolerans gen. nov., sp. nov. are proposed for the mesophilic and moderately thermophilic isolates, respectively, with the respective type strains T23(T) (=DSM 19497(T)=ATCC BAA-1647(T)) and Y005(T) (=DSM 19514(T)=ATCC BAA-1645(T)). PMID:19406797

Johnson, D Barrie; Bacelar-Nicolau, Paula; Okibe, Naoko; Thomas, Angharad; Hallberg, Kevin B

2009-05-01

69

Synthetic and Enhanced Vision Systems for NextGen (SEVS) Simulation and Flight Test Performance Evaluation.  

National Technical Information Service (NTIS)

The Synthetic and Enhanced Vision Systems for NextGen (SEVS) simulation and flight tests are jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA). The flight tests wer...

K. J. Shelton K. K. Ellis L. J. Kramer S. A. Rehfeld

2012-01-01

70

78 FR 28940 - Ninth Meeting: RTCA Next Gen Advisory Committee (NAC)  

Federal Register 2010, 2011, 2012, 2013

...of Meeting and Introduction of NAC Members--Chairman Bill Ayer, Chairman, Alaska Air Group Official Statement of Designated...February 7, 2013 Meeting Summary Chairman's Report--Chairman Ayer FAA Report--Mr. Huerta FAA NextGen Performance...

2013-05-16

71

Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat, and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinibacter gen. nov., Terrisporobacter gen. nov. and Asaccharospora gen. nov.  

PubMed

A Gram-positive staining, rod-shaped, non-motile, spore-forming obligately anaerobic bacterium, designated CRIBT, was isolated from the gastro-intestinal tract of a rat and characterized. The major cellular fatty acids of strain CRIBT were saturated and unsaturated straight-chain C12-C19 fatty acids, with C16:0 being the predominant fatty acid. The polar lipid profile comprised six glycolipids, four phospholipids and one lipid that did not stain with any of the specific spray reagents used. The only quinone was MK-6. The predominating cell-wall sugars were glucose and galactose. The peptidoglycan type of strain CRIBT was A1? lanthionine-direct. The genomic DNA G+C content of strain CRIBT was 28.1 mol%. On the basis of 16S rRNA gene sequence similarity, strain CRIBT was most closely related to a number of species of the genus Clostridium, including Clostridium lituseburense (97.2%), Clostridium glycolicum (96.2%), Clostridium mayombei (96.2%), Clostridium bartlettii (96.0%) and Clostridium irregulare (95.5%). All these species show very low 16S rRNA gene sequence similarity (<85%) to the type strain of Clostridium butyricum, the type species of the genus Clostridium. DNA-DNA hybridization with closely related reference strains indicated reassociation values below 32%. On the basis of phenotypic and genetic studies, a novel genus, Romboutsia gen. nov., is proposed. The novel isolate CRIBT (=DSM 25109T=NIZO 4048T) is proposed as the type strain of the type species, Romboutsia ilealis gen. nov., sp. nov., of the proposed novel genus. It is proposed that C. lituseburense is transferred to this genus as Romboutsia lituseburensis comb. nov. Furthermore, the reclassification into novel genera is proposed for C. bartlettii, as Intestinibacter bartlettii gen. nov., comb. nov. (type species of the genus), C. glycolicum, as Terrisporobacter glycolicus gen. nov., comb. nov. (type species of the genus), C. mayombei, as Terrisporobacter mayombei gen. nov., comb. nov., and C. irregulare, as Asaccharospora irregularis gen. nov., comb. nov. (type species of the genus), on the basis of additional data collected in this study. In addition, an emendation of the species Peptostreptococcus anaerobius and the order Eubacteriales is provided. PMID:24480908

Gerritsen, Jacoline; Fuentes, Susana; Grievink, Wieke; van Niftrik, Laura; Tindall, Brian J; Timmerman, Harro M; Rijkers, Ger T; Smidt, Hauke

2014-05-01

72

GenIE: an intelligent system for writing genetic counseling patient letters.  

PubMed

We are developing GenIE, a prototype intelligent system to create first drafts of genetic counseling patient letters. GenIE will apply natural language generation techniques to construct the first draft of a letter for subsequent review and editing, if needed, by the genetic counselor. For purposes of knowledge acquisition, we have been analyzing a corpus of patient letters. Based on the corpus analysis we are developing a knowledge base and text generation strategies. PMID:16779256

Green, Nancy

2005-01-01

73

Mobile payment models and their implications for NextGen MSPs  

Microsoft Academic Search

Purpose – This paper aims to provide a first overview of important implications of payment models for next-generation mobile service platforms (NextGen MSPs). Design\\/methodology\\/approach – The starting point of the paper is an existing set of mobile payment models. These models are modified and expanded on in order to be able to highlight implications for NextGen MSPs. Findings – The

Michaël Van Bossuyt; Leo Van Hove

2007-01-01

74

Preliminary Investigation of Civil Tiltrotor in NextGen Airspace  

NASA Technical Reports Server (NTRS)

Presentation intro: Tiltrotor aircraft have long been envisioned as being a potentially viable means of commercial aviation transport. Preliminary results from an ongoing study into the operational and technological considerations of Civil Tiltrotor (CTR) operation in the Next Generation airspace, circa the 2025 time-frame, are presented and discussed. In particular, a fleet of CTR aircraft has been conceptually designed. The performance characteristics of this CTR fleet was subsequently translated into BADA (Base of Aircraft DAta) models that could be used as input to emulate CTR aircraft operations in the ACES and AvTerminal airspace and terminal area simulation tools. A network of nine North-Eastern corridor airports is the focus of the airspace simulation effort; the results from this airport network viII then be extrapolated to provide insights into systemic impact of CTRs on the National Airspace System (NAS). Future work will also be detailed as to attempts to model the systemic effects of noise and emissions from this fleet of new aircraft as well as assess their leveraged impact on public service missions, in time of need, such as major regional/national disaster relief efforts. The ideal outcome of this study is a set of results whereby Next Gen airspace CONOPs can be refined to reflect potential CTR capabilities and, conversely, CTR technology development efforts can be better informed as to key performance requirement thresholds needed to be met in order to successfully introduce these aircraft into civilian aviation operation.

Young, Larry A.; Salvano, Dan; Wright, Ken; Chung, William; Young, Ray; Miller, David; Paris, Alfanso; Gao, Huina; Cheng, Victor

2010-01-01

75

Puniceibacterium antarcticum gen. nov., sp. nov., isolated from seawater.  

PubMed

A Gram-reaction-negative, aerobic, non-flagellated, rod-shaped bacterium, designated strain SM1211T, was isolated from Antarctic seawater. The isolate grew at 4-35 °C and with 0-10% (w/v) NaCl. It could produce bacteriochlorophyll a, but did not reduce nitrate to nitrite or hydrolyse DNA. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain SM1211T constituted a distinct phylogenetic line within the family Rhodobacteraceae and was closely related to species in the genera Litorimicrobium, Leisingera, Seohaeicola and Phaeobacter with 95.1-96.0% similarities. The predominant cellular fatty acid was C18:1?7c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid and two unidentified phospholipids. The genomic DNA G+C content of strain SM1211T was 60.7 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain SM1211T is considered to represent a novel species in a new genus within the family Rhodobacteraceae, for which the name Puniceibacterium antarcticum gen. nov., sp. nov. is proposed. The type strain of Puniceibacterium antarcticum is SM1211T (=CCTCC AB 2013147T=KACC 16875T). PMID:24478211

Liu, Chang; Zhang, Xi-Ying; Su, Hai-Nan; Zhou, Ming-Yang; Chen, Bo; Li, Hai; Chen, Xiu-Lan; Zhao, Dian-Li; Zhou, Bai-Cheng; Shi, Mei; Zhang, Yu-Zhong

2014-05-01

76

Diaminobutyricibacter tongyongensis gen. nov., sp. nov. and Homoserinibacter gongjuensis gen. nov., sp. nov. Belong to the Family Microbacteriaceae.  

PubMed

Two bacterial strains, KIS66-7(T) and 5GH26-15(T), were isolated from soil samples collected in the South Korean cities of Tongyong and Gongju, respectively. Both strains were aerobic, Gram-stain-positive, mesophilic, flagellated, and rodshaped. A phylogenetic analysis revealed that both strains belonged to the family Microbacteriaceae of the phylum Actinobacteria. The 16S rRNA gene sequence of strain KIS66-7(T) had the highest similarities with those of Labedella gwakjiensis KSW2-17(T) (97.3%), Cryobacterium psychrophilum DSM 4854T (97.2%), Leifsonia lichenia 2Sb(T) (97.2%), Leifsonia naganoensis JCM 10592(T) (97.0%), and Cryobacterium mesophilum MSL-15(T) (97.0%). Strain 5GH26-15(T) showed the highest sequence similarities with Leifsonia psychrotolerans LI1T (97.4%) and Schumannella luteola KHIAT (97.1%). The 16S rRNA gene sequence from KIS66-7(T) exhibited 96.4% similarity with that from 5GH26-15(T). Strain KIS66-7(T) contained a B2? type peptidoglycan structure with D-DAB as the diamino acid; MK-13, MK-12, and MK-14 as the respiratory quinones; ai-C15:0, ai-C17:0, and i-C16:0 as the major cellular fatty acids; and diphosphatidylglycerol, phatidylglycerol, and glycolipids as the predominant polar lipids. Strain 5GH26-15T had a B2? type peptidoglycan structure with D-DAB as the diamino acid; MK-14 and MK-13 as the respiratory quinones; ai-C15:0, i-C16:0, and ai-C{vn17:0} as the major cellular fatty acids; and diphosphatidylglycerol, phatidylglycerol, and glycolipids as the predominant polar lipids. Both strains had low DNA-DNA hybridization values (<40%) with closely related taxa. Based on our polyphasic taxonomic characterization, we propose that strains KIS66-7(T) and 5GH26-15(T) represent novel genera and species, for which we propose the names Diaminobutyricibacter tongyongensis gen. nov., sp. nov. (type strain KIS66-7(T)=KACC 15515(T)=NBRC 108724(T)) and Homoserinibacter gongjuensis gen. nov., sp. nov. (type strain 5GH26-15(T)=KACC 15524(T)=NBRC 108755(T)) within the family Microbacteriaceae. PMID:24535740

Kim, Soo-Jin; Ahn, Jae-Hyung; Weon, Hang-Yeon; Hamada, Moriyuki; Suzuki, Ken-Ichiro; Kwon, Soon-Wo

2014-06-01

77

MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data  

Microsoft Academic Search

MAPPFinder is a tool that creates a global gene-expression profile across all areas of biology by integrating the annotations of the Gene Ontology (GO) Project with the free software package GenMAPP http:\\/\\/www.GenMAPP.org. The results are displayed in a searchable browser, allowing the user to rapidly identify GO terms with over-represented numbers of gene-expression changes. Clicking on GO terms generates GenMAPP

Scott W. Doniger; Nathan Salomonis; Kam D Dahlquist; Karen Vranizan; Steven C Lawlor; Bruce R Conklin

2003-01-01

78

Critical Issues on Materials for Gen-IV Reactors  

SciTech Connect

Within the LDRD on 'Critical Issues on Materials for Gen-IV Reactors' basic thermodynamics of the Fe-Cr alloy and accurate atomistic modeling were used to help develop the capability to predict hardening, swelling and embrittlement using the paradigm of Multiscale Materials Modeling. Approaches at atomistic and mesoscale levels were linked to build-up the first steps in an integrated modeling platform that seeks to relate in a near-term effort dislocation dynamics to polycrystal plasticity. The requirements originated in the reactor systems under consideration today for future sources of nuclear energy. These requirements are beyond the present day performance of nuclear materials and calls for the development of new, high temperature, radiation resistant materials. Fe-Cr alloys with 9-12% Cr content are the base matrix of advanced ferritic/martensitic (FM) steels envisaged as fuel cladding and structural components of Gen-IV reactors. Predictive tools are needed to calculate structural and mechanical properties of these steels. This project represents a contribution in that direction. The synergy between the continuous progress of parallel computing and the spectacular advances in the theoretical framework that describes materials have lead to a significant advance in our comprehension of materials properties and their mechanical behavior. We took this progress to our advantage and within this LDRD were able to provide a detailed physical understanding of iron-chromium alloys microstructural behavior. By combining ab-initio simulations, many-body interatomic potential development, and mesoscale dislocation dynamics we were able to describe their microstructure evolution. For the first time in the case of Fe-Cr alloys, atomistic and mesoscale were merged and the first steps taken towards incorporating ordering and precipitation effects into dislocation dynamics (DD) simulations. Molecular dynamics (MD) studies of the transport of self-interstitial, vacancy and point defect clusters in concentrated Fe-Cr alloys were performed for future diffusion data calculations. A recently developed parallel MC code with displacement allowed us to predict the evolution of the defect microstructures, local chemistry changes, grain boundary segregation and precipitation resulting from radiation enhanced diffusion. We showed that grain boundaries, dislocations and free surfaces are not preferential for alpha-prime precipitation, and explained experimental observations of short-range order (SRO) in Fe-rich FeCr alloys. Our atomistic studies of dislocation hardening allowed us to obtain dislocation mobility functions for BCC pure iron and Fe-Cr and determine for FCC metals the dislocation interaction with precipitates with a description to be used in Dislocation Dynamic (DD) codes. A Synchronous parallel Kinetic Monte Carlo code was developed and tested which promises to expand the range of applicability of kMC simulations. This LDRD furthered the limits of the available science on the thermodynamic and mechanic behavior of metallic alloys and extended the application of physically-based multiscale materials modeling to cases of severe temperature and neutron fluence conditions in advanced future nuclear reactors. The report is organized as follows: after a brief introduction, we present the research activities, and results obtained. We give recommendations on future LLNL activities that may contribute to the progress in this area, together with examples of possible research lines to be supported.

Caro, M; Marian, J; Martinez, E; Erhart, P

2009-02-27

79

Falsochrobactrum ovis gen. nov., sp. nov., isolated from a sheep.  

PubMed

A Gram-stain-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (B1315(T)) was isolated from the placenta of a sheep with abortion. On the basis of 16S rRNA gene sequence analyses the strain was assigned to the Brucella-Ochrobactrum-Paenochrobactrum-Pseudochrobactrum group with 94.5-94.8?%, 94.3-96.1?%, 95.0-95.1?%, and 95.9-96.1?% sequence similarities to type strains of species of the four genera, respectively. Phylogenetic trees indicated a close relationship to the type strains of Ochrobactrum gallinifaecis and Ochrobactrum oryzae (95.9 and 96.1?% sequence similarity, respectively). Chemotaxonomic data confirmed the allocation of strain B1315(T) to the family Brucellaceae (quinone system: ubiquinone Q-10 and major fatty acids: C18?:?1?7c and C19?:?0 cyclo ?8c). The polar lipid profile contained the major lipids diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and the unidentified but unique phospholipid PL7. The polyamine pattern of strain B1315(T) contained the major polyamines spermidine and putrescine. On the basis of the 16S rRNA gene and recA sequence phylogeny and chemotaxonomic data strain B1315(T) was clearly different from the genera Brucella, Ochrobactrum, Paenochrobactrum and Pseudochrobactrum. On the basis of these data we propose the novel genus Falsochrobactrum gen. nov. with the type species Falsochrobactrum ovis sp. nov. with the type strain B1315(T) (?=?CCM 8460(T)?=?LMG 27356(T.)) The taxonomic allocation of O. gallinifaecis, which grouped inconsistently together with strain B1315(T) on the basis of 16S rRNA gene sequence data, but shows the chemotaxonomic features of the genus Ochrobactrum, remains to be clarified. PMID:23687057

Kämpfer, Peter; Glaeser, Stefanie; Busse, Hans-Jürgen; Eisenberg, Tobias; Scholz, Holger

2013-10-01

80

Nibribacter koreensis gen. nov., sp. nov., isolated from estuarine water.  

PubMed

A Gram-reaction-negative, rod-shaped, non-motile, red-pigmented bacterium, designated strain GSR3061(T), was isolated from a water sample of the Mangyung estuary enclosed by the Saemangeum Embankment in JEOLlabuk-do of South Korea, and characterized using a polyphasic approach. 16S rRNA gene sequence analysis of strain GSR3061(T) indicated that the isolate belonged to the phylum Bacteroidetes and exhibited similarity levels of 94.7?% to Rufibacter tibetensis NRRL B-51285(T), 92.4?% to Adhaeribacter terreus KACC 14257(T) and 91.9?% to Pontibacter korlensis KACC 15371(T). Growth was observed at 15-40 °C and pH 6.5-9.5. The major cellular fatty acids of the novel strain were summed feature 4 (comprising iso-C17?:?1 I and/or anteiso-C17?:?1 B), iso-C15?:?0, C17?:?1?6c and iso-C16?:?1 H. Flexirubin-type pigments were absent. The DNA G+C content of strain GSR3061(T) was 44.9 mol% and the major quinone was MK-7. The polar lipid profile consisted mainly of phosphatidylethanolamine; three unidentified lipids, two unknown aminolipids, two unknown phospholipids, an unknown aminophospholipid and an unknown glycolipid were also present. On the basis of the evidence presented, it is concluded that strain GSR3061(T) represents a novel species of a new genus, for which the name Nibribacter koreensis gen. nov., sp. nov. is proposed. The type strain of Nibribacter koreensis is GSR3061(T) (?=?KACC 16450(T)?=?JCM 17917(T)). PMID:23934250

Kang, Ji Young; Chun, Jeesun; Jahng, Kwang Yeop

2013-12-01

81

Undibacterium pigrum gen. nov., sp. nov., isolated from drinking water.  

PubMed

Two Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacteria (strains CCUG 49009(T) and CCUG 49012), both isolated from drinking water, were characterized. On the basis of chemotaxonomic data [major ubiquinone, Q-8; predominant polyamines, putrescine and 2-hydroxyputrescine; major polar lipids, phosphatidylethanolamine, moderate amounts of diphosphatidylglycerol and phosphatidylglycerol and minor amounts of three aminolipids and phosphatidylserine; major fatty acids, C(16 : 0) and summed feature 3 (C(16 : 1) omega 7c/C(15 : 0) iso 2-OH)] and 16S rRNA gene sequence similarities, both strains clearly belong to the family Oxalobacteraceae of the Betaproteobacteria. 16S rRNA gene sequence similarities with members of the most closely related genera of this group (Herminiimonas, Massilia, Duganella, Telluria, Herbaspirillum, Janthinobacterium, Naxibacter and Paucimonas) were less than 96.5 % for both strains. The two strains also shared a relatively low 16S rRNA gene sequence similarity (96.8 %). Although phylogenetic analysis based on 16S rRNA gene sequence similarities clearly showed that the two organisms formed a separate branch, their phenotypes (including chemotaxonomic features) were hardly distinguishable and showed high similarities to those reported for the most closely related genera. On the basis of DNA-DNA hybridization results, the two strains were shown to represent separate species (sharing only 20 % DNA-DNA relatedness), but they could not be clearly differentiated phenotypically from each other. It is evident that these organisms represent a new genus, Undibacterium gen. nov., with one species, Undibacterium pigrum sp. nov. The type strain of Undibacterium pigrum is strain CCUG 49009(T) (=CIP 109318(T)). Strain CCUG 49012 (=CIP 108976) probably represents a second species of this genus, but is described here as a second genomovar of this species because of the lack of differentiating characters. PMID:17625185

Kämpfer, Peter; Rosselló-Mora, Ramon; Hermansson, Malte; Persson, Frank; Huber, Birgit; Falsen, Enevold; Busse, Hans-Jürgen

2007-07-01

82

Safety Sufficiency for NextGen: Assessment of Selected Existing Safety Methods, Tools, Processes, and Regulations  

NASA Technical Reports Server (NTRS)

NextGen is a complex socio-technical system and, in many ways, it is expected to be more complex than the current system. It is vital to assess the safety impact of the NextGen elements (technologies, systems, and procedures) in a rigorous and systematic way and to ensure that they do not compromise safety. In this study, the NextGen elements in the form of Operational Improvements (OIs), Enablers, Research Activities, Development Activities, and Policy Issues were identified. The overall hazard situation in NextGen was outlined; a high-level hazard analysis was conducted with respect to multiple elements in a representative NextGen OI known as OI-0349 (Automation Support for Separation Management); and the hazards resulting from the highly dynamic complexity involved in an OI-0349 scenario were illustrated. A selected but representative set of the existing safety methods, tools, processes, and regulations was then reviewed and analyzed regarding whether they are sufficient to assess safety in the elements of that OI and ensure that safety will not be compromised and whether they might incur intolerably high costs.

Xu, Xidong; Ulrey, Mike L.; Brown, John A.; Mast, James; Lapis, Mary B.

2013-01-01

83

Initial Investigation of Operational Concept Elements for NASA's NextGen-Airportal Project Research  

NASA Technical Reports Server (NTRS)

The NextGen-Airportal Project is organized into three research focus areas: Safe and Efficient Surface Operations, Coordinated Arrival/Departure Operations Management, and Airportal Transition and Integration Management. The content in this document was derived from an examination of constraints and problems at airports for accommodating future increases in air traffic, and from an examination of capabilities envisioned for NextGen. The concepts are organized around categories of constraints and problems and therefore do not precisely match, but generally reflect, the research focus areas. The concepts provide a framework for defining and coordinating research activities that are, and will be, conducted by the NextGen-Airportal Project. The concepts will help the research activities function as an integrated set focused on future needs for airport operations and will aid aligning the research activities with NextGen key capabilities. The concepts are presented as concept elements with more detailed sub-elements under each concept element. For each concept element, the following topics are discussed: constraints and problems being addressed, benefit descriptions, required technology and infrastructure, and an initial list of potential research topics. Concept content will be updated and more detail added as the research progresses. The concepts are focused on enhancing airportal capacity and efficiency in a timeframe 20 to 25 years in the future, which is similar to NextGen's timeframe.

Lohr, Gary; Lee, Jonathan; Poage, James L.; Tobias, Leonard

2009-01-01

84

Tools for Designing, Evaluating, and Certifying NextGen Technologies and Procedures: Automation Roles and Responsibilities  

NASA Technical Reports Server (NTRS)

Barbara Kanki from NASA Ames Research Center will discuss research that focuses on the collaborations between pilots, air traffic controllers and dispatchers that will change in NextGen systems as automation increases and roles and responsibilities change. The approach taken by this NASA Ames team is to build a collaborative systems assessment template (CSAT) based on detailed task descriptions within each system to establish a baseline of the current operations. The collaborative content and context are delineated through the review of regulatory and advisory materials, policies, procedures and documented practices as augmented by field observations and interviews. The CSAT is developed to aid the assessment of key human factors and performance tradeoffs that result from considering different collaborative arrangements under NextGen system changes. In theory, the CSAT product may be applied to any NextGen application (such as Trajectory Based Operations) with specified ground and aircraft capabilities.

Kanki, Barbara G.

2011-01-01

85

Magnetic behavior in Cr2@Gen (1?n?12) clusters: A density functional investigation  

NASA Astrophysics Data System (ADS)

With a goal to produce magnetic moment in Cr2 Doped Gen clusters which will be useful for practical applications, we have considered the structure and magnetic properties of Pure Germanium clusters and substitutionally doped it with Cr dimer to produce Cr2@Gen clusters. As the first step of calculation, geometrical optimizations of the nanoclusters have been done. These optimized geometries have been used in calculate the average binding energy per atom (BE), HOMO-LUMO gap and hence the relative stability of the clusters. These parameters have been demonstrated as structural and electronic properties of the clusters. Gap between highest occupied molecular orbital and lowest unoccupied molecular orbital indicate cluster to be a potential motif for generating magnetic cluster assembled materials. Based on these values a comparative study on different sized clusters has been done in order to understand the origin of structures, electronic and magnetic properties of Cr2@Gen nanoclusters.

Dhaka, Kapil; Trivedi, Ravi; Bandyopadhyay, Debashis

2014-04-01

86

A low-power dual-clock strategy for digital circuits of EPC Gen2 RFID tag  

Microsoft Academic Search

Power consumption is critical to the performance of EPC Gen2 RFID tags. System clock frequency of tags should be as low as possible to reduce the power consumption and still conform to the protocol. This paper analyses the impact of different clock strategies on digital circuits of EPC Gen2 tag. An error shift approach is proposed to reduce the backscatter

Qiasi Luo; Li Guo; Qing Li; Gang Zhang; Junyu Wang

2009-01-01

87

Discourses in conflict: The relationship between Gen Y pre-service teachers, digital technologies and lifelong learning  

Microsoft Academic Search

This paper analyses Gen Y pre-service primary school teachers' conceptualisations of lifelong learning. It is situated within a context of improving the provision and delivery of pre-service teacher education. This paper argues that Gen Y's understanding of lifelong learning has been influenced by their engagements with digital technologies and that while they may have appropriated the Discourse of change in

Sharn Donnison

88

75 FR 1052 - Terra-Gen Dixie Valley, LLC; TGP Dixie Development Company, LLC; New York Canyon, LLC; Notice of...  

Federal Register 2010, 2011, 2012, 2013

...Energy Regulatory Commission [Docket No. EL10-29-000] Terra-Gen Dixie Valley, LLC; TGP Dixie Development Company, LLC...December 30, 2009. Take notice that on December 24, 2009, Terra-Gen Dixie Valley, LLC, TGP Dixie Development Company,...

2010-01-08

89

77 FR 56839 - GenOn Marsh Landing, LLC; Supplemental Notice That Initial Market-Based Rate Filing Includes...  

Federal Register 2010, 2011, 2012, 2013

...Regulatory Commission [Docket No. ER12-2545-000] GenOn Marsh Landing, LLC; Supplemental Notice That Initial Market-Based Rate...notice in the above-referenced proceeding, of GenOn Marsh Landing, LLC's application for market-based rate authority,...

2012-09-14

90

Das klinische Spektrum von Fertilitätsstörungen durch Mutationen im CFTR-Gen  

Microsoft Academic Search

Zusammenfassung  \\u000a \\u000a Mehr als 95 % der mnnlichen Betroffenen einer Mukoviszidose sind aufgrund einer congenitalen beidseitigen Vas-deferens-Aplasie\\u000a infertil. Mutationen im CFTR-Gen haben je nach Art und Lokalisation im Gen sehr unterschiedliche physiologische Konsequenzen\\u000a und finden sich nicht nur bei Patienten mit dem Vollbild der Mukoviszidose, sondern auch bei verschiedenen Formen der obstruktiven\\u000a Azoospermie wie der isolierten, ein- oder beidseitigen Vas-deferens-Aplasie und

Manfred Stuhrmann

1998-01-01

91

Biochemical and Molecular Characterization of the Gentisate Transporter GenK in Corynebacterium glutamicum  

PubMed Central

Background Gentisate (2,5-dihydroxybenzoate) is a key ring-cleavage substrate involved in various aromatic compounds degradation. Corynebacterium glutamicum ATCC13032 is capable of growing on gentisate and genK was proposed to encode a transporter involved in this utilization by its disruption in the restriction-deficient mutant RES167. Its biochemical characterization by uptake assay using [14C]-labeled gentisate has not been previously reported. Methodology/Principal Findings In this study, biochemical characterization of GenK by uptake assays with [14C]-labeled substrates demonstrated that it specifically transported gentisate into the cells with Vmax and Km of 3.06±0.16 nmol/min/mg of dry weight and 10.71±0.11 µM respectively, and no activity was detected for either benzoate or 3-hydoxybenzoate. When GenK was absent in strain RES167 ?genK, it retained 85% of its original transport activity at pH 6.5 compared to that of strain RES167. However, it lost 79% and 88% activity at pH 7.5 and 8.0, respectively. A number of competing substrates, including 3-hydroxybenzoate, benzoate, protocatechuate and catechol, significantly inhibited gentisate uptake by more than 40%. Through site-directed mutagenesis, eight amino acid residues of GenK, Asp-54, Asp-57 and Arg-386 in the hydrophobic transmembrane regions and Arg-103, Trp-309, Asp-312, Arg-313 and Ile-317 in the hydrophilic cytoplasmic loops were shown to be important for gentisate transport. When conserved residues Asp-54 and Asp-57 respectively were changed to glutamate, both mutants retained approximately 50% activity and were able to partially complement the ability of strain RES167 ?genK to grow on gentisate. Conclusions/Significance Our results demonstrate that GenK is an active gentisate transporter in Corynebacterium glutamicum ATCC13032. The GenK-mediated gentisate transport was also shown to be a limiting step for the gentisate utilization by this strain. This enhances our understanding of gentisate transport in the microbial degradation of aromatic compounds.

Xu, Ying; Wang, Song-He; Chao, Hong-Jun; Liu, Shuang-Jiang; Zhou, Ning-Yi

2012-01-01

92

Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov.  

PubMed Central

Senegalemassilia anaerobia strain JC110T sp.nov. is the type strain of Senegalemassilia anaerobia gen. nov., sp. nov., the type species of a new genus within the Coriobacteriaceae family, Senegalemassilia gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. S. anaerobia is a Gram-positive anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,383,131 bp long genome contains 1,932 protein-coding and 58 RNA genes.

Lagier, Jean-Christophe; Elkarkouri, Khalid; Rivet, Romain; Couderc, Carine; Raoult, Didier; Fournier, Pierre-Edouard

2013-01-01

93

Novel anamorphic mite-associated fungi belonging to the Ustilaginomycetes: Meira geulakonigii gen. nov., sp. nov., Meira argovae sp. nov. and Acaromyces ingoldii gen. nov., sp. nov.  

PubMed

Three novel mite-associated basidiomycetous species are described in two new anamorph genera as Meira geulakonigii gen. nov., sp. nov. (type CBS 110052(T)=NRRL Y-27483(T)=AS 004(T)), Meira argovae sp. nov. (type CBS 110053(T)=NRRL Y-27482(T)=AS 005(T)) and Acaromyces ingoldii gen. nov., sp. nov. (type CBS 110050(T)=NRRL Y-27484(T)=AS 001(T)). Morphologically, these fungi are similar to the yeast-like fungi classified in the Ustilaginales, such as Pseudozyma species. However, analysis of the D1/D2 domain of the LSU rDNA suggests that they belong to two different lineages within the Exobasidiomycetidae of the Ustilaginomycetes (Basidiomycota). Furthermore, these fungi may be of interest for the biocontrol of mites, as they reduced mite numbers by approximately 80 % after inoculation. PMID:13130065

Boekhout, Teun; Theelen, Bart; Houbraken, Jos; Robert, Vincent; Scorzetti, Gloria; Gafni, Aviva; Gerson, Uri; Sztejnberg, Abraham

2003-09-01

94

Aethosolenia laselvensis gen. nov., sp. nov., a new eupodoid mite from Costa Rica (Acari: Prostigmata)  

Microsoft Academic Search

A new genus and species of eupodoid mite is described from leaf litter of lowland tropical rainforest in Costa Rica. Aethosolenia laselvensis gen. nov., sp. nov. possesses a combination of morphological characters which does not match the current definition for any eupodoid family. The decision to place it in the Eupodidae is discussed and an amended definition of the family

ANNE S. BAKER; EVERT E. LINDQUIST

2002-01-01

95

Mining metadata from unidentified ITS sequences in GenBank: A case study in Inocybe (Basidiomycota)  

Microsoft Academic Search

BACKGROUND: The lack of reference sequences from well-identified mycorrhizal fungi often poses a challenge to the inference of taxonomic affiliation of sequences from environmental samples, and many environmental sequences are thus left unidentified. Such unidentified sequences belonging to the widely distributed ectomycorrhizal fungal genus Inocybe (Basidiomycota) were retrieved from GenBank and divided into species that were identified in a phylogenetic

Martin Ryberg; R Henrik Nilsson; Erik Kristiansson; Mats Töpel; Stig Jacobsson; Ellen Larsson

2008-01-01

96

Preliminary Results From High Temperature Scoping Irradiation Experiments Of Selected Gen IV Structural Metallic Materials  

Microsoft Academic Search

The performance of Generation IV reactors as a class will be determined by the behavior of advanced engineering materials. In the case of materials utilized for reactor internals and pressure vessels, the effects of irradiation are major issues. The environmental conditions for most of the Gen IV reactors are generally beyond present day reactor technology, especially as regards the combinations

Randy K Nanstad; David A McClintock; David T Hoelzer

2007-01-01

97

Sigecheres Brittae Gen. Et SP. Nov., a Parasitic Copepod from the Polychaete Sige Fusigera Malmgren.  

National Technical Information Service (NTIS)

Both sexes of Sigecheres brittae gen. et sp. nov., a parasitic copepod found on the phyllodocid polychaete Sige fusigera in Danish waters, are described and figured. The systematic relations of the new genus are discussed and it is concluded that it is ra...

J. Bresciani

1964-01-01

98

GWAS in a Box: Statistical and Visual Analytics of Structured Associations via GenAMap  

PubMed Central

With the continuous improvement in genotyping and molecular phenotyping technology and the decreasing typing cost, it is expected that in a few years, more and more clinical studies of complex diseases will recruit thousands of individuals for pan-omic genetic association analyses. Hence, there is a great need for algorithms and software tools that could scale up to the whole omic level, integrate different omic data, leverage rich structure information, and be easily accessible to non-technical users. We present GenAMap, an interactive analytics software platform that 1) automates the execution of principled machine learning methods that detect genome- and phenome-wide associations among genotypes, gene expression data, and clinical or other macroscopic traits, and 2) provides new visualization tools specifically designed to aid in the exploration of association mapping results. Algorithmically, GenAMap is based on a new paradigm for GWAS and PheWAS analysis, termed structured association mapping, which leverages various structures in the omic data. We demonstrate the function of GenAMap via a case study of the Brem and Kruglyak yeast dataset, and then apply it on a comprehensive eQTL analysis of the NIH heterogeneous stock mice dataset and report some interesting findings. GenAMap is available from http://sailing.cs.cmu.edu/genamap.

Xing, Eric P.; Curtis, Ross E.; Schoenherr, Georg; Lee, Seunghak; Yin, Junming; Puniyani, Kriti; Wu, Wei; Kinnaird, Peter

2014-01-01

99

Acantholachesilla gen. n. (Psocodea:'Psocoptera': Lachesillidae: Eolachesillinae: Graphocaeciliini) from Valle del Cauca, Colombia.  

PubMed

Acantholachesilla saltoensis gen. et sp. n. is described from Valle del Cauca, Colombia, in the Lachesillidae, tribe Graphocaeciliini (Eolachesillinae). The genus is related to Dagualachesilla and Dagualachesilloides that occur in the same area, differing from them in the male clunial projection, phallosome, and female subgenital plate and gonapophyses. PMID:24989767

Aldrete, Alfonso N García; Manchola, Oscar Fernando Saenz; Obando, Ranulfo González

2014-01-01

100

Doratomantispa burmanica n. gen., n. sp. (Neuroptera: Mantispidae), a new genus of mantidflies in Burmese amber  

Microsoft Academic Search

A new genus and new species of mantidflies, Doratomantispa burmanica n. gen., n. sp. (Neuroptera: Mantispidae), is described from Burmese amber. Diagnostic characters of the new genus are small body size, trichosors present around entire wing margin except basally, protarsus 5-segmented with paired, simple claws but no aroleum, profemur bearing six cuticular spines, inner surface of protibia with row of

George Poinar Jr; Ron Buckley

2011-01-01

101

InGen of creative production in the health sciences: A workbook companion to innovation generation  

Microsoft Academic Search

InGen of Creative Production in the Health Sciences is a compendium of innovative thinking exercises for individuals and groups, derived from an eclectic array of practical guides for professionals in a variety of fields. Segmented into five subcategories across twenty two chapters, the effort seeks to make techniques for increasing innovative problem solving more accessible to a diverse audience of

Michael Goodman

2011-01-01

102

FDP-GEN Federal Demonstration Project (FDP) General Terms and Conditions  

NSF Publications Database

Title : FDP-GEN Federal Demonstration Project (FDP) General Terms and Conditions Type : Grant Conditions NSF Org: OD / LPA Date : January 7, 1994 File : fdpgen Federal Demonstration Project General Terms and Conditions Article Subject 1. Recipient Responsibilities and Federal Requirements . 5 17. Use of U.S.-Flag Air Carriers . 7 28. Research Involving Recombinant DNA Molecules.

103

Left Ventricular Systolic Dysfunction in a Biracial Sample of Hypertensive Adults The HyperGEN Study  

Microsoft Academic Search

To determine the prevalence and correlates of left ventricular systolic dysfunction in hypertensive patients in a biracial population-based sample, clinical evaluation and echocardiography were performed in 2086 participants in the Hypertension Genetic Epidemiology Network (HyperGEN) examination; 86% had normal ejection fraction (.54%), 10% had mild ventricular dysfunction (ejection fraction 41% to 54%), and 4% had severe ventricular dysfunction (ejection fraction

Richard B. Devereux; Jonathan N. Bella; Vittorio Palmieri; Albert Oberman; Dalane W. Kitzman; Paul N. Hopkins; D. C. Rao; Derek Morgan; Mary Paranicas; Dawn Fishman; Donna K. Arnett

104

Extending Validated Human Performance Models to Explore NextGen Concepts  

NASA Technical Reports Server (NTRS)

To meet the expected increases in air traffic demands, NASA and FAA are researching and developing Next Generation Air Transportation System (NextGen) concepts. NextGen will require substantial increases in the data available to pilots on the flight deck (e.g., weather,wake, traffic trajectory predictions, etc.) to support more precise and closely coordinated operations (e.g., self-separation, RNAV/RNP, and closely spaced parallel operations, CSPOs). These NextGen procedures and operations, along with the pilot's roles and responsibilities, must be designed with consideration of the pilot's capabilities and limitations. Failure to do so will leave the pilots, and thus the entire aviation system, vulnerable to error. A validated Man-machine Integration and design Analysis System (MIDAS) v5 model was extended to evaluate anticipated changes to flight deck and controller roles and responsibilities in NextGen approach and Land operations. Compared to conditions when the controllers are responsible for separation on decent to land phase of flight, the output from these model predictions suggest that the flight deck response time to detect the lead aircraft blunder will decrease, pilot scans to the navigation display will increase, and workload will increase.

Gore, Brian Francis; Hooey, Becky Lee; Mahlstedt, Eric; Foyle, David C.

2012-01-01

105

Single phase permanent-magnet generator with low armature reaction for induction heating gen sets  

Microsoft Academic Search

The paper presents a single phase, slotless axial flux permanent magnet synchronous machine for induction heating gen sets. A full scale prototype of the machine (110 kVA, 400 Hz, 690 A) has been designed and subsequently analyzed through FEM analysis (FEA). Induced current distributions in the permanent magnets (PMs) and in the rotors are also calculated through FEA and it

F. Caricchi; F. Maradei; G. De Donato; F. Giulii Capponi

2008-01-01

106

Distribution, paleoecology, paleoclimatology, and botanical affinity of the Eocene pollen genus Diporoconia n. gen  

Microsoft Academic Search

Diporoconia n. gen. is proposed for diporate subisopolar smooth to perforate pollen grains having annuli or tumescence. Diporoconia iszkaszentgyoergyi (Kedves) n. comb. (the type species), D. nnewiensis (Jan du Chêne et al.) n. comb., and D. spp. 1 and 2 are included in the genus. Distinctive characters of the pollen are the large pores that are at the ends of

N. O. Frederiksen; V. D. Wiggins; I. K. Ferguson; J. Dransfield; C. M. Ager

1985-01-01

107

FutureGen: Pathway to Near-Zero Emissions and Sustainable Energy  

SciTech Connect

This presentation will highlight the U.S. Department of Energy’s (DOE) FutureGen project ? a $1 billion government-industry partnership to design, build, and operate a near-zero emissions coal-fueled power plant. The lead organization for the FutureGen initiative is the National Energy Technology Laboratory (NETL), a multi-purpose laboratory operated by the U.S. DOE’s Office of Fossil Energy. NETL has a mission to conduct R&D from fundamental science to technology demonstration for resolving the environmental, supply, and reliability constraints of producing and using fossil energy resources. The commercial-scale FutureGen R&D facility is a pathway toward future fossil-energy power plants that will produce hydrogen and electricity while nearly eliminating emissions, including carbon dioxide. The 275-megawatt FutureGen plant will initiate operations around 2012 and employ advanced coal gasification technology integrated with combined cycle electricity generation, hydrogen production, and carbon capture and sequestration. Low carbon emissions would be achieved by integrating CO2 capture and sequestration operations with the power plant.

Zitney, S.E.; Sarkus, T.A

2007-11-04

108

KiteGen project: control as key technology for a quantum leap in wind energy generators  

Microsoft Academic Search

The paper investigates the control of tethered airfoils in order to devise a new class of wind generators, indicated as KiteGen, able to overcome the main limitations of the present aeolian technology based on wind mills. A model taken from the literature is used to simulate the dynamic of a kite whose lines are suitably pulled by a control unit.

M. Canale; L. Fagiano; M. Milanese; M. Ippolito

2007-01-01

109

FutureGen: Stepping-Stone to Sustainable Fossil-Fuel Power Generation.  

National Technical Information Service (NTIS)

This presentation will highlight the U.S. Department of Energy's FutureGen Initiative. The nearly $1 billion government-industry project is a stepping-stone toward future coal-fired power plants that will produce hydrogen and electricity with zero-emissio...

S. E. Zitney

2006-01-01

110

Functional Allocation for Ground-Based Automated Separation Assurance in NextGen.  

National Technical Information Service (NTIS)

As part of an ongoing research effort into functional allocation in a NextGen environment, a controller-in-the-loop study on ground-based automated separation assurance was conducted at NASA Ames' Airspace Operations Laboratory in February 2010. Participa...

C. Brasil C. Cabrall J. Homola J. Mercer L. Martin T. Prevot

2010-01-01

111

Dayao gen. n. of the subtribe Tyrina (Coleoptera, Staphylinidae, Pselaphinae) from South China  

PubMed Central

Abstract Dayao pengzhongi gen. et sp. n. is described and illustrated based on the material collected in Guangxi Province, South China. The genus is placed in the oriental ‘Pselaphodes complex’ of genera of the subtribe Tyrina and its taxonomic placement is discussed.

Yin, Zi-Wei; Li, Li-Zhen; Zhao, Mei-Jun

2011-01-01

112

The GenTechnique Project: Developing an Open Environment for Learning Molecular Genetics.  

ERIC Educational Resources Information Center

The GenTechnique project at Washington State University uses a networked learning environment for molecular genetics learning. The project is developing courseware featuring animation, hyper-link controls, and interactive self-assessment exercises focusing on fundamental concepts. The first pilot course featured a Web-based module on DNA…

Calza, R. E.; Meade, J. T.

1998-01-01

113

Working with Gen Y Teachers: Dealing with a Changing Teacher Workforce  

ERIC Educational Resources Information Center

A significant change is coming to American classrooms. As Baby Boomer teachers retire and are replaced by members of Generation Y (born between 1977 and 1995) there is growing evidence that they come from a far different set of experiences, experiences that will shape their lives and their careers (Coggins, 2008). Members of Gen Y share several…

Williamson, Ronald; Meyer-Looze, Catherine

2010-01-01

114

Environmental Information for the U.S. Next Generation Air Transportation System (NextGen)  

NASA Astrophysics Data System (ADS)

It is estimated that weather is responsible for approximately 70% of all air traffic delays and cancellations in the United States. Annually, this produces an overall economic loss of nearly 40B. The FAA and NASA have determined that weather impacts and other environmental constraints on the U.S. National Airspace System (NAS) will increase to the point of system unsustainability unless the NAS is radically transformed. A Next Generation Air Transportation System (NextGen) is planned to accommodate the anticipated demand for increased system capacity and the super-density operations that this transformation will entail. The heart of the environmental information component that is being developed for NextGen will be a 4-dimensional data cube which will include a single authoritative source comprising probabilistic weather information for NextGen Air Traffic Management (ATM) systems. Aviation weather constraints and safety hazards typically comprise meso-scale, storm-scale and microscale observables that can significantly impact both terminal and enroute aviation operations. With these operational impacts in mind, functional and performance requirements for the NextGen weather system were established which require significant improvements in observation and forecasting capabilities. This will include satellite observations from geostationary and/or polar-orbiting hyperspectral sounders, multi-spectral imagers, lightning mappers, space weather monitors and other environmental observing systems. It will also require improved in situ and remotely sensed observations from ground-based and airborne systems. These observations will be used to better understand and to develop forecasting applications for convective weather, in-flight icing, turbulence, ceilings and visibility, volcanic ash, space weather and the environmental impacts of aviation. Cutting-edge collaborative research efforts and results from NASA, NOAA and the FAA which address these phenomena are summarized. In 2003, a Joint Planning and Development Office (JPDO) was established by public law to meet the significant challenges that NextGen presents. JPDO partners were chartered which include, but are not limited to, the Federal Aviation Administration (FAA), the National Oceanic and Atmospheric Administration (NOAA), the National Aeronautics and Space Administration (NASA), the Department of Defense (DOD) and broad elements of academia and the aviation industry. This paper provides the aviation meteorology community with useful insight on salient NextGen environmental information requirements that have been developed by the JPDO Weather Working Group's Environmental Information Team. These efforts will help to define observation and forecast systems needed to support NextGen and to develop the operational applications for NextGen aviation weather information. Another major goal of this paper is to inform the international weather community of our research progress and plans for NextGen, to foster research collaboration with our colleagues, and to exchange information to maximize success of NextGen, SESAR and related initiatives world-wide.

Murray, J.; Miner, C.; Pace, D.; Minnis, P.; Mecikalski, J.; Feltz, W.; Johnson, D.; Iskendarian, H.; Haynes, J.

2009-09-01

115

GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework.  

PubMed

GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada. GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis. PMID:23922841

Parks, Donovan H; Mankowski, Timothy; Zangooei, Somayyeh; Porter, Michael S; Armanini, David G; Baird, Donald J; Langille, Morgan G I; Beiko, Robert G

2013-01-01

116

GenGIS 2: Geospatial Analysis of Traditional and Genetic Biodiversity, with New Gradient Algorithms and an Extensible Plugin Framework  

PubMed Central

GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada. GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis.

Parks, Donovan H.; Mankowski, Timothy; Zangooei, Somayyeh; Porter, Michael S.; Armanini, David G.; Baird, Donald J.; Langille, Morgan G. I.; Beiko, Robert G.

2013-01-01

117

Transduction of Photoreceptors With Equine Infectious Anemia Virus Lentiviral Vectors: Safety and Biodistribution of StarGen for Stargardt Disease  

PubMed Central

Purpose. StarGen is an equine infectious anemia virus (EIAV)-based lentiviral vector that expresses the photoreceptor-specific adenosine triphosphate (ATP)-binding cassette transporter (ABCA4) protein that is mutated in Stargardt disease (STGD1), a juvenile macular dystrophy. EIAV vectors are able to efficiently transduce rod and cone photoreceptors in addition to retinal pigment epithelium in the adult macaque and rabbit retina following subretinal delivery. The safety and biodistribution of StarGen following subretinal delivery in macaques and rabbits was assessed. Methods. Regular ophthalmic examinations, IOP measurements, ERG responses, and histopathology were carried out in both species to compare control and vector-treated eyes. Tissue and fluid samples were obtained to evaluate the persistence, biodistribution, and shedding of the vector following subretinal delivery. Results. Ophthalmic examinations revealed a slightly higher level of inflammation in StarGen compared with control treated eyes in both species. However, inflammation was transient and no overt toxicity was observed in StarGen treated eyes and there were no abnormal clinical findings. There was no StarGen-associated rise in IOP or abnormal ERG response in either rabbits or macaques. Histopathologic examination of the eyes did not reveal any detrimental changes resulting from subretinal administration of StarGen. Although antibodies to StarGen vector components were detected in rabbit but not macaque serum, this immunologic response did not result in any long-term toxicity. Biodistribution analysis demonstrated that the StarGen vector was restricted to the ocular compartment. Conclusions. In summary, these studies demonstrate StarGen to be well tolerated and localized following subretinal administration.

Binley, Katie; Widdowson, Peter; Loader, Julie; Kelleher, Michelle; Iqball, Sharifah; Ferrige, Georgina; de Belin, Jackie; Carlucci, Marie; Angell-Manning, Diana; Hurst, Felicity; Ellis, Scott; Miskin, James; Fernandes, Alcides; Wong, Paul; Allikmets, Rando; Bergstrom, Christopher; Aaberg, Thomas; Yan, Jiong; Kong, Jian; Gouras, Peter; Prefontaine, Annick; Vezina, Mark; Bussieres, Martin; Naylor, Stuart; Mitrophanous, Kyriacos A.

2013-01-01

118

YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps  

PubMed Central

Comparative genetic maps are used in examination of genome organization, detection of conserved gene order, and exploration of marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability of users' own genetic mapping between 2 or more map sets. Users' genetic map data and optional gene annotations are uploaded, either publically or privately, as long as they follow our template which is available in several standard file formats. Data is parsed and loaded into MySQL relational database to be displayed and compared against users' genetic maps or other public data available on YouGenMap. With the highly interactive GUIs, all public data on YouGenMap are maps available for visualization, comparison, search, filtration and download. YouGenMap web tool is available on the website (http://conifergdb.miamioh.edu/yougenmap) with the source-code repository at (http://sourceforge.net/projects/yougenmap/?source=directory).

Batesole, Keith; Wimalanathan, Kokulapalan; Liu, Lin; Zhang, Fan; Echt, Craig S.; Liang, Chun

2014-01-01

119

Mercury: Next-gen Data Analysis and Annotation Pipeline (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)  

ScienceCinema

David Sexton (Baylor) gives a talk titled "Mercury: Next-gen Data Analysis and Annotation Pipeline" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

120

Aradidae from Vietnam III. Trichosomaptera gibbosa n.gen., n.sp., an apterous Carventinae (Hemiptera: Heteroptera: Aradidae) .  

PubMed

A new apterous flat bug genus of the subfamily Carventinae, Trichosomaptera n.gen., is described and illustrated to accommodate gibbosa n. sp. from Vietnam. The species could not be placed in any known genus. PMID:24871183

Pham, Minhlan; Bai, Xiaoshuan; Heiss, Ernst; Cai, Wanzhi

2014-01-01

121

75 FR 5780 - Green Borders Geothermal, LLC, Complainant, v. Terra-Gen Dixie Valley, LLC, Respondent; Notice of...  

Federal Register 2010, 2011, 2012, 2013

...Regulatory Commission [Docket No. EL10-36-000] Green Borders Geothermal, LLC, Complainant, v. Terra-Gen...2010. Take notice that on January 25, 2010, Green Borders Geothermal, LLC (Green Borders) filed a formal complaint against...

2010-02-04

122

Clinical Evaluation of the Gen-Probe Amplified Direct Test for Detection of Mycobacterium tuberculosis Complex Organisms in Cerebrospinal Fluid  

Microsoft Academic Search

Eighty-four cerebrospinal fluid (CSF) samples from different children who presented with signs and symp- toms of meningitis were evaluated for the presence of Mycobacterium tuberculosis complex organisms by the Gen- Probe Amplified Mycobacterium tuberculosis Direct Test (MTD; Gen-Probe, San Diego, Calif.). All CSF samples had negative acid-fast smears by the Ziehl-Neelsen staining method. M. tuberculosis was recovered from five samples.

ANNE M. LANG; JESUS FERIS-IGLESIAS; CHABELA PENA; JACQUELINE F. SANCHEZ; LESLIE STOCKMAN; PAUL RYS; GLENN D. ROBERTS; NANCY K. HENRY; DAVID H. PERSING; FRANKLIN R. COCKERILL; Robert Reid

1998-01-01

123

Parametric Modeling of the Safety Effects of NextGen Terminal Maneuvering Area Conflict Scenarios  

NASA Technical Reports Server (NTRS)

The goal of this work was to analytically identify and quantify the issues, challenges, technical hurdles, and pilot-vehicle interface issues associated with conflict detection and resolution (CD&R)in emerging operational concepts for a NextGen terminal aneuvering area, including surface operations. To this end, the work entailed analytical and trade studies focused on modeling the achievable safety benefits of different CD&R strategies and concepts in the current and future airport environment. In addition, crew-vehicle interface and pilot performance enhancements and potential issues were analyzed based on review of envisioned NextGen operations, expected equipage advances, and human factors expertise. The results of perturbation analysis, which quantify the high-level performance impact of changes to key parameters such as median response time and surveillance position error, show that the analytical model developed could be useful in making technology investment decisions.

Rogers, William H.; Waldron, Timothy P.; Stroiney, Steven R.

2011-01-01

124

jPopGen Suite: population genetic analysis of DNA polymorphism from nucleotide sequences with errors.  

PubMed

1. Next-generation sequencing (NGS) is being increasingly used in ecological and evolutionary studies. Though promising, NGS is known to be error-prone. Sequencing error can cause significant bias for population genetic analysis of a sequence sample.2. We present jPopGen Suite, an integrated tool for population genetic analysis of DNA polymorphisms from nucleotide sequences. It is specially designed for data with a non-negligible error rate, although it serves well for "error-free" data. It implements several methods for estimating the population mutation rate, population growth rate, and conducting neutrality tests.3. jPopGen Suite facilitates the population genetic analysis of NGS data in various applications, and is freely available for non-commercial users at http://sites.google.com/site/jpopgen/. PMID:22905315

Liu, Xiaoming

2012-08-01

125

Gen 2.0 Mixer/Ejector Nozzle Test at LSAF June 1995 to July 1996  

NASA Technical Reports Server (NTRS)

Testing of the HSCT Generation 2.0 nozzle model hardware was conducted at the Boeing Low Speed Aeroacoustic Facility, LSAF. Concurrent measurements of noise and thrust were made at critical takeoff design conditions for a variety of mixer/ejector model hardware. Design variables such as suppressor area ratio, mixer area ratio, liner type and thickness, ejector length, lobe penetration, and mixer chute shape were tested. Parallel testing was conducted at G.E.'s Cell 41 acoustic free jet facility to augment the LSAF test. The results from the Gen 2.0 testing are being used to help shape the current nozzle baseline configuration and guide the efforts in the upcoming Generation 2.5 and 3.0 nozzle tests. The Gen 2.0 results have been included in the total airplane system studies conducted at MDC and Boeing to provide updated noise and thrust performance estimates.

Arney, L. D.; Sandquist, D. L.; Forsyth, D. W.; Lidstone, G. L.; Long-Davis, Mary Jo (Technical Monitor)

2005-01-01

126

Identification and Characterization of Key Human Performance Issues and Research in the Next Generation Air Transportation System (NextGen)  

NASA Technical Reports Server (NTRS)

This report identifies key human-performance-related issues associated with Next Generation Air Transportation System (NextGen) research in the NASA NextGen-Airspace Project. Four Research Focus Areas (RFAs) in the NextGen-Airspace Project - namely Separation Assurance (SA), Airspace Super Density Operations (ASDO), Traffic Flow Management (TFM), and Dynamic Airspace Configuration (DAC) - were examined closely. In the course of the research, it was determined that the identified human performance issues needed to be analyzed in the context of NextGen operations rather than through basic human factors research. The main gaps in human factors research in NextGen were found in the need for accurate identification of key human-systems related issues within the context of specific NextGen concepts and better design of the operational requirements for those concepts. By focusing on human-system related issues for individual concepts, key human performance issues for the four RFAs were identified and described in this report. In addition, mixed equipage airspace with components of two RFAs were characterized to illustrate potential human performance issues that arise from the integration of multiple concepts.

Lee, Paul U.; Sheridan, Tom; Poage, james L.; Martin, Lynne Hazel; Jobe, Kimberly K.

2010-01-01

127

StreamGen: A Workload Generation Tool for Distributed Information Flow Applications  

Microsoft Academic Search

This paper presents the StreamGen load generator, which is targeted at distributed information flow applications. These include the event streaming services used in wide-area publish\\/subscribe systems or in operational information systems, the data streaming services used in remote visualization or collaboration, and the continuous data streams occurring in download services. Running across heterogeneous distributed platforms, these services are implemented by

Mohamed S. Mansour; Matthew Wolf; Karsten Schwan

2004-01-01

128

Enhancing Security of EPCglobal Gen2 RFID Tag against Traceability and Cloning  

Microsoft Academic Search

In this paper, we present a synchronization-based communication protocol for RFID devices. We focus on the EPCGlobal Class-1 Gen-2 RFID tag which supports only simple cryptographic primitives like Pseudo-random Number Generator (PRNG) and Cyclic Redundancy Code (CRC). Our protocol is secure in a sense that it prevents the cloned tags and malicious readers from impersonating and abusing legitimate tags, respectively.

Dang Nguyen Duc; Jaemin Park; Hyunrok Lee; Kwangjo Kim

129

Sinobaatar gen. nov.: First multituberculate from the Jehol Biota of Liaoning, Northeast China  

Microsoft Academic Search

A multituberculate skeleton from the Lower Cretaceous Yixian Formation at Dawangzhangzi, Lingyuan City, Liaoning Province,\\u000a Northeast China, provides new morphological information for early multituberculates. The specimen is the holotype of Sinobaatar lingyuanensis gen. et sp. nov. It has a narrow skull that lacks the superorbital crest or postorbital process. The dental formula is 3.?.5.2\\/1.0.3.2.\\u000a The dental morphology, especially that of

Yaoming Hu; Yuanqing Wang

2002-01-01

130

Complexity analysis of the Next Gen Air Traffic Management System: trajectory based operations.  

PubMed

According to Federal Aviation Administration traffic predictions currently our Air Traffic Management (ATM) system is operating at 150 percent capacity; forecasting that within the next two decades, the traffic with increase to a staggering 250 percent [17]. This will require a major redesign of our system. Today's ATM system is complex. It is designed to safely, economically, and efficiently provide air traffic services through the cost-effective provision of facilities and seamless services in collaboration with multiple agents however, contrary the vision, the system is loosely integrated and is suffering tremendously from antiquated equipment and saturated airways. The new Next Generation (Next Gen) ATM system is designed to transform the current system into an agile, robust and responsive set of operations that are designed to safely manage the growing needs of the projected increasingly complex, diverse set of air transportation system users and massive projected worldwide traffic rates. This new revolutionary technology-centric system is dynamically complex and is much more sophisticated than it's soon to be predecessor. ATM system failures could yield large scale catastrophic consequences as it is a safety critical system. This work will attempt to describe complexity and the complex nature of the NextGen ATM system and Trajectory Based Operational. Complex human factors interactions within Next Gen will be analyzed using a proposed dual experimental approach designed to identify hazards, gaps and elicit emergent hazards that would not be visible if conducted in isolation. Suggestions will be made along with a proposal for future human factors research in the TBO safety critical Next Gen environment. PMID:22317416

Lyons, Rhonda

2012-01-01

131

[14] Statistics for ChIP?chip and DNase Hypersensitivity Experiments on NimbleGen Arrays  

Microsoft Academic Search

Data obtained from high?density oligonucleotide tiling arrays present new computational challenges for users. This chapter presents ACME (Algorithm for Capturing Microarray Enrichment), a computer program developed for the analysis of data obtained using NimbleGen?tiled microarrays. ACME identifies signals or “peaks” in tiled array data using a simple sliding window and threshold strategy and assigns a probability value (p value) to

Peter C. Scacheri; Gregory E. Crawford; Sean Davis

2006-01-01

132

NMPP: a user-customized NimbleGen microarray data processing pipeline  

Microsoft Academic Search

Summary: NMPP package is a bundle of user-customized tools based on established algorithms and methods to process self- designed NimbleGen microarray data. It features a command-line- based integrative processing procedure that comprises five major functional components, namely the raw microarray data parsing and integrating module, the array spatial effect smoothing and visualization module, the probe-level multi-array normalization module, the gene

Xiangfeng Wang; Hang He; Lei Li; Runsheng Chen; Xing Wang Deng; Songgang Li

2006-01-01

133

GEN IV MATERIALS HANDBOOK BETA RELEASE FOR STRUCTURAL AND FUNCTIONAL EVALUATION  

SciTech Connect

Development of the Gen IV Materials Handbook is briefly summarized up to date. Current status of the Handbook website construction is described. The developed Handbook components and access control of the beta version are discussed for the present evaluation release. Detailed instructions and examples are given to provide guidance for evaluators to browse the constructed parts and use all the currently developed functionalities of the Handbook in evaluation.

Ren, Weiju [ORNL] [ORNL; Luttrell, Claire [ORNL] [ORNL

2006-09-12

134

Dual-track CCS stakeholder engagement: Lessons learned from FutureGen in Illinois  

USGS Publications Warehouse

FutureGen, as originally planned, was to be the world's first coal-fueled, near-zero emissions power plant with fully integrated, 90% carbon capture and storage (CCS). From conception through siting and design, it enjoyed strong support from multiple stakeholder groups, which benefited the overall project. Understanding the stakeholder engagement process for this project provides valuable insights into the design of stakeholder programs for future CCS projects. FutureGen is one of few projects worldwide that used open competition for siting both the power plant and storage reservoir. Most site proposals were coordinated by State governments. It was unique in this and other respects relative to the site selection method used on other DOE-supported projects. At the time of site selection, FutureGen was the largest proposed facility designed to combine an integrated gasification combined cycle (IGCC) coal-fueled power plant with a CCS system. Stakeholder engagement by states and the industry consortium responsible for siting, designing, building, and operating the facility took place simultaneously and on parallel tracks. On one track were states spearheading state-wide site assessments to identify candidate sites that they wanted to propose for consideration. On the other track was a public-private partnership between an industry consortium of thirteen coal companies and electric utilities that comprised the FutureGen Alliance (Alliance) and the U.S. Department of Energy (DOE). The partnership was based on a cooperative agreement signed by both parties, which assigned the lead for siting to the Alliance. This paper describes the stakeholder engagement strategies used on both of these tracks and provides examples from the engagement process using the Illinois semi-finalist sites. ?? 2011 Published by Elsevier Ltd.

Hund, G.; Greenberg, S. E.

2011-01-01

135

Demissolinea novaeguineensis gen. et sp. nov. (Perciformes: Trichiuridae), a new hairtail from New Guinea  

Microsoft Academic Search

Demissolinea novaeguineensis gen. et sp. nov., a new trichiurid fish described on the basis of two specimens collected off Dolak Island, southwestern\\u000a New Guinea, lacks a caudal fin, the tail instead tapering into a hairlike process. Although this condition also exists in\\u000a the genera Eupleurogrammus, Lepturacanthus, Tentoriceps, and Trichiurus, the new genus and species can be easily distinguished from all

Andi Iqbal Burhanuddin; Yukio Iwatsuki

2003-01-01

136

Biomek-3000 and GenPlex SNP Genotyping in Forensic Genetics  

Microsoft Academic Search

Single nucleotide polymorphism genotyping provides a supplement for conventional short tandem repeats-based kits currently used for human identification. GenPlex (Applied Biosystems (AB), Foster City, CA) is an SNP-genotyping kit based on a multiplex of 48 informative, autosomal SNPs from the SNPforID Consortium. Our objective was to setup, implement, and validate a small and affordable automated liquid-handling robot for forensic casework

Michael Stangegaard; Carmen Tomas; Anders J. Hansen; Rune Frank-Hansen; Claus Børsting; Niels Morling

2008-01-01

137

A System-on-Chip EPC Gen2 Passive UHF RFID Tag With Embedded Temperature Sensor  

Microsoft Academic Search

This paper presents a system-on-chip passive RFID tag with an embedded temperature sensor for the EPC Gen-2 protocol in the 900-MHz UHF frequency band. A dual-path clock generator is proposed to support both applications with either very accurate link frequency or very low power consumption. On-chip temperature sensing is accomplished with a time-readout scheme to reduce the power consumption. Moreover,

Jun Yin; Jun Yi; M. K. Law; Yunxiao Ling; Man Chiu Lee; Kwok Ping Ng; Bo Gao; H. C. Luong; A. Bermak; Mansun Chan; Wing-Hung Ki; Chi-Ying Tsui; M. Yuen

2010-01-01

138

Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along  

Microsoft Academic Search

Abstract Motivation: Seq-Gen is a program,that will simulate the evolution of nucleotide sequences along a phylogeny, using common,models,of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. Nucleotide frequencies and other parameters,of the model may be given and site-specific rate heterogeneity can also be incorporated in a number,of ways. Any number,of trees

Andrew Rambaut; Nicholas C. Grassly

139

Development of an Enhanced GenVARR™ (Generator Volt Ampere Reactive Reserve) System  

SciTech Connect

Transmission system operators require near real time knowledge of reactive power capability to reliably operate large electric power transmission systems. Reactive power produced by, or capable of being produced by, a power generator is often estimated based on a series of mega volt amperes (MVA) capability curves for the generator. These curves indicate the ability of the generator to produce real and reactive power under a variety of conditions. In transmission planning and operating studies, it is often assumed, based on estimates for these capability curves, that the generator can provide its rated MVA capability output when needed for system stability However, generators may not always operate at levels depicted by the maximum MVA capability curve due to present constraints. Transmission system operators utilizing the generators’ capability curves for operation decisions regarding transmission system stability or for planning horizons may overestimate the capability of the generators to supply reactive power when required. Southern Company has enhanced GenVARR(TM), the system of plant data query, retrieval, and analysis and calculates the actual – not estimated -- remaining reactive power output capability. The remaining reactive output is considered spinning reserve and is displayed graphically to transmission control center and generating plant operators to identify real time VAR limits. GenVARR is capable of aggregating generators from a defined region, or other user selectable combinations, to represent the available reserves that the operators are specifically interested in. GenVARR(TM) has been put into live production operation and is expected to significantly improve the overall visibility of the reactive reserve capability of the system. This new version of GenVARR(TM) significantly enhances the products structure and performance, and enables links to other key transmission system operation tools.

Schatz, Joe E.

2009-03-12

140

Rahiolisaurus gujaratensis, n. gen. n. sp., A New Abelisaurid Theropod from the Late Cretaceous of India  

NASA Astrophysics Data System (ADS)

Systematic excavations in the fluvial mudstone unit of the Upper Cretaceous Lameta Formation near Rahioli village in Kheda District, Gujarat, have yielded a large-bodied (~8 m long) abelisaurid theropod, Rahiolisaurus gujaratensis, gen. et sp. nov. Abundant skeletal remains represent this new genus and species. Rahiolisaurus provides novel information on foot morphology, hitherto little known in other abelisaurids. Rahiolisaurus gujaratensis is a gracile and slender-limbed abelisaurid that appears to be a distinctive taxon from the sympatric species Rajasaurus narmadensis.

Novas, Fernando E.; Chatterjee, Sankar; Rudra, Dhiraj K.; Datta, P. M.

141

GOParGenPy: a high throughput method to generate Gene Ontology data matrices  

PubMed Central

Background Gene Ontology (GO) is a popular standard in the annotation of gene products and provides information related to genes across all species. The structure of GO is dynamic and is updated on a daily basis. However, the popular existing methods use outdated versions of GO. Moreover, these tools are slow to process large datasets consisting of more than 20,000 genes. Results We have developed GOParGenPy, a platform independent software tool to generate the binary data matrix showing the GO class membership, including parental classes, of a set of GO annotated genes. GOParGenPy is at least an order of magnitude faster than popular tools for Gene Ontology analysis and it can handle larger datasets than the existing tools. It can use any available version of the GO structure and allows the user to select the source of GO annotation. GO structure selection is critical for analysis, as we show that GO classes have rapid turnover between different GO structure releases. Conclusions GOParGenPy is an easy to use software tool which can generate sparse or full binary matrices from GO annotated gene sets. The obtained binary matrix can then be used with any analysis environment and with any analysis methods.

2013-01-01

142

Enhanced and Synthetic Vision for Terminal Maneuvering Area NextGen Operations  

NASA Technical Reports Server (NTRS)

Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment with equivalent efficiency as visual operations. To meet this potential, research is needed for effective technology development and implementation of regulatory and design guidance to support introduction and use of SVS/EFVS advanced cockpit vision technologies in Next Generation Air Transportation System (NextGen) operations. A fixed-base pilot-in-the-loop simulation test was conducted at NASA Langley Research Center that evaluated the use of SVS/EFVS in NextGen low visibility ground (taxi) operations and approach/landing operations. Twelve crews flew approach and landing operations in a simulated NextGen Chicago O Hare environment. Various scenarios tested the potential for EFVS for operations in visibility as low as 1000 ft runway visibility range (RVR) and SVS to enable lower decision heights (DH) than can currently be flown today. Expanding the EFVS visual segment from DH to the runway in visibilities as low as 1000 RVR appears to be viable as touchdown performance was excellent without any workload penalties noted for the EFVS concept tested. A lower DH to 150 ft and/or possibly reduced visibility minima by virtue of SVS equipage appears to be viable when implemented on a Head-Up Display, but the landing data suggests further study for head-down implementations.

Kramer, Lynda J.; Bailey, Randall E.; Ellis, Kyle K. E.; Norman, R. Michael; Williams, Steven P.; Arthur, Jarvis J., III; Shelton, Kevin J.; Prinzel, Lawrence J., III

2011-01-01

143

Hungatella effluvii gen. nov., sp. nov., an obligately anaerobic bacterium isolated from an effluent treatment plant, and reclassification of Clostridium hathewayi as Hungatella hathewayi gen. nov., comb. nov.  

PubMed

A Gram-stain-positive, rod-shaped, spore-forming and strictly anaerobic bacterium, designated UB-B.2(T), was isolated from an industrial effluent anaerobic digester sample. It grew optimally at 30 °C and pH 7.0. Comparative analysis of the 16S rRNA gene sequence confirmed that strain UB-B.2(T) was closely related to Clostridium hathewayi DSM 13479(T) (97.84% similarity), a member of rRNA gene cluster XIVa of the genus Clostridium, and formed a coherent cluster with other related members of the Blautia (Clostridium) coccoides rRNA group in phylogenetic analyses. The end products of glucose fermentation by strain UB-B.2(T) were acetate and propionate. The G+C content of the DNA was 51.4 mol%. Although strain UB-B.2(T) showed 97.8% 16S rRNA gene sequence identity to the type strain of C. hathewayi, it exhibited only 38.4% relatedness at the whole-genome level. It also showed differences from its closest phylogenetic relative, C. hathewayi DSM 13479(T), in phenotypic characteristics such as hydrolysis of aesculin, starch and urea and fermentation end products. Both strains showed phenotypic differences from the members of rRNA gene cluster XIVa of the genus Clostridium. Based on these differences, C. hathewayi DSM 13479(T) and strain UB-B.2(T) were identified as representatives of a new genus of the family Clostridiaceae. Thus, we propose the reclassification of Clostridium hathewayi as Hungatella hathewayi gen. nov., comb. nov., the type species of the new genus (type strain DSM 13479(T)?=?CCUG 43506(T)?=?MTCC 10951(T)). Strain UB-B.2(T) (?=?MTCC 11101(T)?=?DSM 24995(T)) is assigned to the novel species Hungatella effluvii gen. nov., sp. nov as the type strain. PMID:24186873

Kaur, Sukhpreet; Yawar, Mir; Kumar, P Anil; Suresh, K

2014-03-01

144

Psychroserpens burtonensis gen. nov., sp. nov., and Gelidibacter algens gen. nov., sp. nov., psychrophilic bacteria isolated from antarctic lacustrine and sea ice habitats.  

PubMed

Psychrophilic, yellow-pigmented, seawater-requiring bacteria isolated from the pycnocline of meromictic Burton Lake and from sea ice cores obtained in the Vestfold Hills (68 degrees S, 78 degrees E) in eastern Antarctica were characterized. Phenotypic analysis showed that the strains isolated formed two distinct taxa. The first taxon included nonmotile, nutritionally fastidious strains that were isolated from the pycnocline of Burton Lake. The cells of these strains were morphologically variant, ranging from vibrioid to ring shaped to coiled and filamentous; in addition, the strains were unable to metabolise carbohydrates or polysaccharides and had DNA G + C contents of 27 to 29 mol%. The strains of the second taxon, which were isolated from sea ice cores and from ice aigal biomass, were saccharolytic, exhibited rapid gliding motility, were rodlike to filamentous, and had DNA G + C contents of 36 to 38 mol%. A 16S ribosomal DNA (rDNA) sequence analysis revealed that the two Antarctic taxa formed related but distinct lineages within the [Flexibacter] maritimus rRNA branch of the family Flavobacteriacrae. The levels of 16S rDNA sequence similarity between the taxa were 90.5 to 91.3%, while the levels of similarity to other members of the [F.] maritimus rRNA branch were 85 to 90%. The whole-cell lipid profiles of the Antarctic strains were mainly comprised of branched and unbranched monounsaturated C15 to C17 fatty acids. The presence of significant levels of the lipids a 15:1 omega 10c and a17:1 omega 7c appeared to be useful biomarkers for the new Antarctic taxa and for differentiating these organisms from other members of the family Flavobacteriaceae. On the basis of polyphasic taxonomic data we propose that the new taxa are novel bacterial species designated Psychroserpens burtonensis gen. nov., sp. nov. (type strain, ACAM 188) and Gelidibacter algens gen. nov., sp. nov. (type strain, ACAM 536). PMID:9226898

Bowman, J P; McCammon, S A; Brown, J L; Nichols, P D; McMeekin, T A

1997-07-01

145

GenDrux: A biomedical literature search system to identify gene expression-based drug sensitivity in breast cancer  

PubMed Central

Background This paper describes the development of a web-based tool, GenDrux, which extracts and presents (over the Internet) information related to the disease-gene-drug nexus. This information is archived from the relevant biomedical literature using automated methods. GenDrux is designed to alleviate the difficulties of manually processing the vast biomedical literature to identify disease-gene-drug relationships. GenDrux will evolve with the literature without additional algorithmic modifications. Results GenDrux, a pilot system, is developed in the domain of breast cancer and can be accessed at http://www.microarray.uab.edu/drug_gene.pl. GenDrux can be queried based on drug, gene and/or disease name. From over 8,000 relevant abstracts from the biomedical literature related to breast cancer, we have archived a corpus of more than 4,000 articles that depict gene expression-drug activity relationships for breast cancer and related cancers. The archiving process has been automated. Conclusions The successful development, implementation, and evaluation of this and similar systems when created may provide clinicians with a tool for literature management, clinical decision making, thus setting the platform for personalized therapy in the future.

2011-01-01

146

Roles of SLX1-SLX4, MUS81-EME1, and GEN1 in avoiding genome instability and mitotic catastrophe.  

PubMed

The resolution of recombination intermediates containing Holliday junctions (HJs) is critical for genome maintenance and proper chromosome segregation. Three pathways for HJ processing exist in human cells and involve the following enzymes/complexes: BLM-TopoIII?-RMI1-RMI2 (BTR complex), SLX1-SLX4-MUS81-EME1 (SLX-MUS complex), and GEN1. Cycling cells preferentially use the BTR complex for the removal of double HJs in S phase, with SLX-MUS and GEN1 acting at temporally distinct phases of the cell cycle. Cells lacking SLX-MUS and GEN1 exhibit chromosome missegregation, micronucleus formation, and elevated levels of 53BP1-positive G1 nuclear bodies, suggesting that defects in chromosome segregation lead to the transmission of extensive DNA damage to daughter cells. In addition, however, we found that the effects of SLX4, MUS81, and GEN1 depletion extend beyond mitosis, since genome instability is observed throughout all phases of the cell cycle. This is exemplified in the form of impaired replication fork movement and S-phase progression, endogenous checkpoint activation, chromosome segmentation, and multinucleation. In contrast to SLX4, SLX1, the nuclease subunit of the SLX1-SLX4 structure-selective nuclease, plays no role in the replication-related phenotypes associated with SLX4/MUS81 and GEN1 depletion. These observations demonstrate that the SLX1-SLX4 nuclease and the SLX4 scaffold play divergent roles in the maintenance of genome integrity in human cells. PMID:24831703

Sarbajna, Shriparna; Davies, Derek; West, Stephen C

2014-05-15

147

Next Gen NEAR: Near Earth Asteroid Human Robotic Precursor Mission Concept  

NASA Technical Reports Server (NTRS)

Asteroids have long held the attention of the planetary science community. In particular, asteroids that evolve into orbits near that of Earth, called near-Earth objects (NEO), are of high interest as potential targets for exploration due to the relative ease (in terms of delta V) to reach them. NASA's Flexible Path calls for missions and experiments to be conducted as intermediate steps towards the eventual goal of human exploration of Mars; piloted missions to NEOs are such example. A human NEO mission is a valuable exploratory step beyond the Earth-Moon system enhancing capabilities that surpass our current experience, while also developing infrastructure for future mars exploration capabilities. To prepare for a human rendezvous with an NEO, NASA is interested in pursuing a responsible program of robotic NEO precursor missions. Next Gen NEAR is such a mission, building on the NEAR Shoemaker mission experience at the JHU/APL Space Department, to provide an affordable, low risk solution with quick data return. Next Gen NEAR proposes to make measurements needed for human exploration to asteroids: to demonstrate proximity operations, to quantify hazards for human exploration and to characterize an environment at a near-Earth asteroid representative of those that may be future human destinations. The Johns Hopkins University Applied Physics Laboratory has demonstrated exploration-driven mission feasibility by developing a versatile spacecraft design concept using conventional technologies that satisfies a set of science, exploration and mission objectives defined by a concept development team in the summer of 2010. We will describe the mission concept and spacecraft architecture in detail. Configuration options were compared with the mission goals and objectives in order to select the spacecraft design concept that provides the lowest cost, lowest implementation risk, simplest operation and the most benefit for the mission implementation. The Next Gen NEAR spacecraft was designed to support rendezvous with a range of candidate asteroid targets and could easily be launched with one of several NASA launch vehicles. The Falcon 9 launch vehicle supports a Next Gen NEAR launch to target many near-Earth asteroids under consideration that could be reached with a C3 of 18 km2/sec2 or less, and the Atlas V-401 provides added capability supporting launch to NEAs that require more lift capacity while at the same time providing such excess lift capability that another payload of opportunity could be launch in conjunction with Next Gen NEAR. Next Gen NEAR will measure and interact with the target surface in ways never undertaken at an asteroid, and will prepare for first human precursor mission by demonstrating exploration science operations at an accessible NEO. This flexible mission and spacecraft design concept supports target selection based on upcoming Earth-based observations and also provides opportunities for co-manifest & international partnerships. JHU/APL has demonstrated low cost, low risk, high impact missions and this mission will help to prepare NASA for human NEO exploration by combining the best of NASA s human and robotic exploration capabilities.

Rivkin, Andrew S.; Kirby, Karen; Cheng, Andrew F.; Gold, Robert; Kelly, Daniel; Reed, Cheryl; Abell, Paul; Garvin, James; Landis, Rob

2012-01-01

148

Enhanced Flight Vision Systems and Synthetic Vision Systems for NextGen Approach and Landing Operations  

NASA Technical Reports Server (NTRS)

Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment with equivalent efficiency as visual operations. To meet this potential, research is needed for effective technology development and implementation of regulatory standards and design guidance to support introduction and use of SVS/EFVS advanced cockpit vision technologies in Next Generation Air Transportation System (NextGen) operations. A fixed-base pilot-in-the-loop simulation test was conducted at NASA Langley Research Center that evaluated the use of SVS/EFVS in NextGen low visibility approach and landing operations. Twelve crews flew approach and landing operations in a simulated NextGen Chicago O'Hare environment. Various scenarios tested the potential for using EFVS to conduct approach, landing, and roll-out operations in visibility as low as 1000 feet runway visual range (RVR). Also, SVS was tested to evaluate the potential for lowering decision heights (DH) on certain instrument approach procedures below what can be flown today. Expanding the portion of the visual segment in which EFVS can be used in lieu of natural vision from 100 feet above the touchdown zone elevation to touchdown and rollout in visibilities as low as 1000 feet RVR appears to be viable as touchdown performance was acceptable without any apparent workload penalties. A lower DH of 150 feet and/or possibly reduced visibility minima using SVS appears to be viable when implemented on a Head-Up Display, but the landing data suggests further study for head-down implementations.

Kramer, Lynda J.; Bailey, Randall E.; Ellis, Kyle K. E.; Williams, Steven P.; Arthur, Jarvis J., III; Prinzel, Lawrence J., III; Shelton, Kevin J.

2013-01-01

149

Collagen (NeuraGen(®)) nerve conduits and stem cells for peripheral nerve gap repair.  

PubMed

Collagen nerve guides are used clinically for peripheral nerve defects, but their use is generally limited to lesions up to 3cm. In this study we combined collagen conduits with cells as an alternative strategy to support nerve regeneration over longer gaps. In vitro cell adherence to collagen conduits (NeuraGen(®) nerve guides) was assessed by scanning electron microscopy. For in vivo experiments, conduits were seeded with either Schwann cells (SC), SC-like differentiated bone marrow-derived mesenchymal stem cells (dMSC), SC-like differentiated adipose-derived stem cells (dASC) or left empty (control group), conduits were used to bridge a 1cm gap in the rat sciatic nerve and after 2-weeks immunohistochemical analysis was performed to assess axonal regeneration and SC infiltration. The regenerative cells showed good adherence to the collagen walls. Primary SC showed significant improvement in distal stump sprouting. No significant differences in proximal regeneration distances were noticed among experimental groups. dMSC and dASC-loaded conduits showed a diffuse sprouting pattern, while SC-loaded showed an enhanced cone pattern and a typical sprouting along the conduits walls, suggesting an increased affinity for the collagen type I fibrillar structure. NeuraGen(®) guides showed high affinity of regenerative cells and could be used as efficient vehicle for cell delivery. However, surface modifications (e.g. with extracellular matrix molecule peptides) of NeuraGen(®) guides could be used in future tissue-engineering applications to better exploit the cell potential. PMID:24792394

di Summa, Pietro G; Kingham, Paul J; Campisi, Corrado C; Raffoul, Wassim; Kalbermatten, Daniel F

2014-06-20

150

GenSalt: rationale, design, methods and baseline characteristics of study participants.  

PubMed

Hypertension is a complex disorder influenced by genetic and environmental determinants and their interactions. The objectives of the Genetic Epidemiology Network of Salt Sensitivity (GenSalt) are to localize and identify genes related to blood pressure (BP) responses to dietary sodium and potassium intervention. GenSalt utilizes a family feeding-study design. Each family was ascertained through a proband with untreated prehypertension or stage-1 hypertension in rural China. A medical history, lifestyle risk factors and responses to cold pressor tests, were obtained at baseline visits while BP, weight, blood and urine specimens were collected at baseline and follow-up visits. The dietary intervention included a 7-day low-sodium feeding (51.3 mmol/day), a 7-day high-sodium feeding (307.8 mmol/day) and a 7-day high-sodium feeding with an oral potassium supplementation (60 mmol/day). Microsatellite markers for genome-wide linkage scan and single nucleotide polymorphism (SNP) markers in candidate genes will be genotyped. Overall, 3153 participants from 658 families were recruited for GenSalt. The mean systolic and diastolic BPs were 128.0 and 80.3, 111.6 and 71.0, 112.6 and 72.6, 106.6 and 65.3 and 136.7 and 75.0 mm Hg for probands, siblings, spouses, offspring and parents, respectively. The mean urinary excretion of sodium and potassium were 232.5 and 38.6, 222.9 and 38.2, 213.1 and 37.8 and 207.3 and 36.0 mmol/24-h for probands, siblings, spouses and offspring, respectively. Our study will identify novel genes that influence significantly the effect of dietary sodium and potassium intake on BP. This information is useful for development of targeted intervention for the prevention and treatment of hypertension. PMID:17443206

2007-08-01

151

Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov.  

PubMed

The genus Rhizorhapis gen. nov. (to replace the illegitimate genus name Rhizomonas) is proposed for strains of Gram-negative bacteria causing corky root of lettuce, a widespread and important lettuce disease worldwide. Only one species of the genus Rhizomonas was described, Rhizomonas suberifaciens, which was subsequently reclassified as Sphingomonas suberifaciens based on 16S rRNA gene sequences and the presence of sphingoglycolipid in the cell envelope. However, the genus Sphingomonas is so diverse that further reclassification was deemed necessary. Twenty new Rhizorhapis gen. nov.- and Sphingomonas-like isolates were obtained from lettuce or sow thistle roots, or from soil using lettuce seedlings as bait. These and previously reported isolates were characterized in a polyphasic study including 16S rRNA gene sequencing, DNA-DNA hybridization, DNA G+C content, whole-cell fatty acid composition, morphology, substrate oxidation, temperature and pH sensitivity, and pathogenicity to lettuce. The isolates causing lettuce corky root belonged to the genera Rhizorhapis gen. nov., Sphingobium, Sphingopyxis and Rhizorhabdus gen. nov. More specifically, we propose to reclassify Rhizomonas suberifaciens as Rhizorhapis suberifaciens gen. nov., comb. nov. (type strain, CA1(T)?=?LMG 17323(T)?=?ATCC 49355(T)), and also propose the novel species Sphingobium xanthum sp. nov., Sphingobium mellinum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. with the type strains NL9(T) (?=?LMG 12560(T)?=?ATCC 51296(T)), WI4(T) (?=?LMG 11032(T)?=?ATCC 51292(T)) and SP1(T) (?=?LMG 12581(T)?=?ATCC 51289(T)), respectively. Several strains isolated from lettuce roots belonged to the genus Sphingomonas, but none of them were pathogenic. PMID:24436067

Francis, Isolde M; Jochimsen, Kenneth N; De Vos, Paul; van Bruggen, Ariena H C

2014-04-01

152

Gen IV Materials Handbook Functionalities and Operation (4A) Handbook Version 4.0  

SciTech Connect

This document is prepared for navigation and operation of the Gen IV Materials Handbook, with architecture description and new user access initiation instructions. Development rationale and history of the Handbook is summarized. The major development aspects, architecture, and design principles of the Handbook are briefly introduced to provide an overview of its past evolution and future prospects. Detailed instructions are given with examples for navigating the constructed Handbook components and using the main functionalities. Procedures are provided in a step-by-step fashion for Data Upload Managers to upload reports and data files, as well as for new users to initiate Handbook access.

Ren, Weiju [ORNL] [ORNL

2013-09-01

153

Gen IV Materials Handbook Functionalities and Operation (2B) Handbook Version 2.0  

SciTech Connect

This document is prepared for navigation and operation of the Gen IV Materials Handbook, with architecture description and new user access initiation instructions. Development rationale and history of the Handbook is summarized. The major development aspects, architecture, and design principles of the Handbook are briefly introduced to provide an overview of its past evolution and future prospects. Detailed instructions are given with examples for navigating the constructed Handbook components and using the main functionalities. Procedures are provided in a step-by-step fashion for Data Upload Managers to upload reports and data files, as well as for new users to initiate Handbook access.

Ren, Weiju [ORNL

2011-08-01

154

Evaluation of Gen-Probe's Histoplasma capsulatum and Cryptococcus neoformans AccuProbes.  

PubMed Central

Gen-Probe's DNA probes were evaluated for use in the identification of clinical isolates of Histoplasma capsulatum var. capsulatum and Cryptococcus neoformans. Ninety-five mould-phase fungi were probed, including 41 isolates of H. capsulatum var. capsulatum. Similarly, 98 yeasts, including 42 C. neoformans isolates, were examined by using the C. neoformans DNA probe. In the study, both probes demonstrated 100% specificity and 100% sensitivity. Their use in the clinical laboratory may significantly reduce the time required for definitive identification of fungi.

Huffnagle, K E; Gander, R M

1993-01-01

155

Electromagnetic Interactions GenERalized (EIGER): Applications at Johnson Space Center  

NASA Technical Reports Server (NTRS)

This slide presentation reviews the software framework for the analysis and design of complex electromagnetic systems. The system called Electromagnetic Interactions GenERalized (EIGER) is a hybrid finite element solution for wave equations and deru=ives boundary element solutions for integral equation formulations. Written in Fortran 90 Eiger uses object-oriented design methods to abstract key analysis components. EIGER has been applied to higher order modeling for analysis of antennas to assist in the design of the antennas of a mini-AERCam. EIGER might also be used to model the Ion Cyclotron Resonant heating stage for the VAriable Specific Impulse Magnetoplasma Rocket (VASIMR).

Dobbins, Justin A.; Fink, Patrick W.; Scully, Robert C.

2003-01-01

156

Nuclear Data Needs Supporting Gen-IV Applications - INL Perspective and Initiatives  

SciTech Connect

Studies conducted in connection with the Department of Energy (DOE) Generation IV (Gen-IV) and Advanced Fuel Cycle (AFC) programs show that the transuranic nuclides can strongly influence the neutronic behavior of some advanced nuclear energy systems of interest. Essentially all integral nuclear parameters computed using modern reactor physics codes and data libraries are affected by propagation of uncertainty in the underlying nuclear data used in the computational models. These parameters include: Criticality (multiplication factor) Reactivity feedback coefficients (e.g., Doppler, Coolant Void) Kinetics parameters (e.g., Effective Delayed Neutron Fraction) Reactivity loss during irradiation (Burnup Swing) Peak power value Conversion ratio of sustainable cores Transmutation potential of burner cores Max dpa, maximum helium- and hydrogen-production, etc. Decay heat, radiotoxicity, and neutron and gamma radiation levels However, the necessary cross section information may be unavailable with the required accuracy from the current nuclear databases for some key nuclides of interest. As a specific example, recent sensitivity analyses for the Very High Temperature Gen-IV reactor concept (Taiwo et al, 2005a, Salvatores et al., 2005, Taiwo et al, 2005b), which features a somewhat harder thermal neutron spectrum and a significantly higher fuel burnup target than is the case for standard light-water reactors, show a potential need for improved cross sections for some isotopes, including 238U, 239Pu, 240Pu, 41Pu, and 243Am, primarily in the resonance energy range, in order to satisfy the defined accuracy requirements on key computed integral parameters. Other transuranic nuclides may be of similar importance for some of the other Gen-IV concepts, although the primary needs appear to be currently focused around a few plutonium and americium isotopes. The target accuracies identified in these studies are very stringent and will be a challenge to achieve in many cases. In this article we briefly review the conclusions and recommendations of recent international workshops on nuclear data needs for Gen-IV. Following this is a discussion of two specific activities undertaken by the Idaho National Laboratory (INL) to participate in the international effort to address these needs.

David W. Nigg

2005-07-01

157

Application of part-whole training methods to evaluate when to introduce NextGen air traffic management tools to students.  

PubMed

The Next Generation Air Transportation System (NextGen) will use advanced technologies and new concepts of operation to accommodate projected increases in air travel over the next few decades. Use of NextGen tools requires air traffic controllers (ATCos) to use different procedures than those required to manage NextGen-unequipped aircraft, and ATCos will need to integrate the 2 skill sets when managing a sector consisting of NextGen-equipped and unequipped aircraft. The goal of the present study was to determine the effectiveness of 2 procedures in the training of student controllers to manage both equipage types. We applied a variant of the part-whole training paradigm in the present study. Using a quasi-experimental design, we trained students from 2 different labs of an internship course to manage air traffic with potential NextGen tools concurrent with their traditional training (whole-task group) or after they had time to learn traditional air traffic management skills (part-whole group). Participants were then tested in their ability to manage a simulated sector consisting of different percentages of NextGen-equipped and unequipped aircraft at the mid-term and after the final week of their internship. Results showed that it is better to train students in manual ATCo skills before introducing NextGen tools, unless the students are of higher aptitude. For more skilled students, simultaneously introducing NextGen and manual tools into their curriculum had little negative impact. PMID:24455810

Vu, Kim-Phuong L; Kiken, Ariana; Chiappe, Dan; Strybel, Thomas Z; Battiste, Vernol

2013-01-01

158

FOSSIL MAYFLY COLLECTIONS OF THE MUSEUM FÜR NATURKUNDE, HUMBOLDT UNIVERSITY BERLIN. I. ELECTROLETUS SOLDANI GEN. AND SP. NOV. (EPHEMEROPTERA: AMELETIDAE) FROM THE EOCENE BALTIC AMBER  

Microsoft Academic Search

Electroletus soldani gen . and sp. nov . from Eocene Baltic amber is described and illustrated. The presence of an elongate lateroparapsidal suture of the mesonotum, sublateroscutum and submedioscutum of the mesonotum with traces of the pigmented area, a backwards-stretched medially mesonotal suture, the dissimilar claws and a 5-seg- mented paracercus undoubtedly define the systematic position of Electroletus gen. nov.

Roman J. Godunko; Christian Neumann

2006-01-01

159

GenExp: An Interactive Web-Based Genomic DAS Client with Client-Side Data Rendering  

PubMed Central

Background The Distributed Annotation System (DAS) offers a standard protocol for sharing and integrating annotations on biological sequences. There are more than 1000 DAS sources available and the number is steadily increasing. Clients are an essential part of the DAS system and integrate data from several independent sources in order to create a useful representation to the user. While web-based DAS clients exist, most of them do not have direct interaction capabilities such as dragging and zooming with the mouse. Results Here we present GenExp, a web based and fully interactive visual DAS client. GenExp is a genome oriented DAS client capable of creating informative representations of genomic data zooming out from base level to complete chromosomes. It proposes a novel approach to genomic data rendering and uses the latest HTML5 web technologies to create the data representation inside the client browser. Thanks to client-side rendering most position changes do not need a network request to the server and so responses to zooming and panning are almost immediate. In GenExp it is possible to explore the genome intuitively moving it with the mouse just like geographical map applications. Additionally, in GenExp it is possible to have more than one data viewer at the same time and to save the current state of the application to revisit it later on. Conclusions GenExp is a new interactive web-based client for DAS and addresses some of the short-comings of the existing clients. It uses client-side data rendering techniques resulting in easier genome browsing and exploration. GenExp is open source under the GPL license and it is freely available at http://gralggen.lsi.upc.edu/recerca/genexp.

Gel Moreno, Bernat; Messeguer Peypoch, Xavier

2011-01-01

160

Brockphasma spinifemoralis gen. et spec. nov.: a new phasmid genus and new species of Neohiraseini (Phasmida: Necrosciinae) from Vietnam.  

PubMed

A new genus of stick insects, Brockphasma Ho gen. nov., with the type-species, Brockphasma spinifemoralis Ho, Liu, Bresseel & Constant spec. nov., is described and illustrated from Vietnam. Both sexes, the egg and the first instar nymph are described and figured. Data on the habitat and natural foodplants are provided. Brockphasma Ho gen. nov. is differentiated from other genera in Neohiraseini by spinose occiput, anterior region of mesonotum with a spinose hump and spinose anterodorsal and posterodorsal carinae of femora. A key to the genera of Neohiraseini from Vietnam is given. PMID:24990046

Ho, George Wai-Chun; Liu, Xing-Yue; Bresseel, Joachim; Constant, Jerome

2014-01-01

161

Structural materials for Gen-IV nuclear reactors: Challenges and opportunities  

NASA Astrophysics Data System (ADS)

Generation-IV reactor design concepts envisioned thus far cater toward a common goal of providing safer, longer lasting, proliferation-resistant and economically viable nuclear power plants. The foremost consideration in the successful development and deployment of Gen-IV reactor systems is the performance and reliability issues involving structural materials for both in-core and out-of-core applications. The structural materials need to endure much higher temperatures, higher neutron doses and extremely corrosive environment, which are beyond the experience of the current nuclear power plants. Materials under active consideration for use in different reactor components include various ferritic/martensitic steels, austenitic stainless steels, nickel-base superalloys, ceramics, composites, etc. This paper presents a summary of various Gen-IV reactor concepts, with emphasis on the structural materials issues depending on the specific application areas. This paper also discusses the challenges involved in using the existing materials under both service and off-normal conditions. Tasks become increasingly complex due to the operation of various fundamental phenomena like radiation-induced segregation, radiation-enhanced diffusion, precipitation, interactions between impurity elements and radiation-produced defects, swelling, helium generation and so forth. Further, high temperature capability (e.g. creep properties) of these materials is a critical, performance-limiting factor. It is demonstrated that novel alloy and microstructural design approaches coupled with new materials processing and fabrication techniques may mitigate the challenges, and the optimum system performance may be achieved under much demanding conditions.

Murty, K. L.; Charit, I.

2008-12-01

162

GenSSI: a software toolbox for structural identifiability analysis of biological models  

PubMed Central

Summary: Mathematical modeling has a key role in systems biology. Model building is often regarded as an iterative loop involving several tasks, among which the estimation of unknown parameters of the model from a certain set of experimental data is of central importance. This problem of parameter estimation has many possible pitfalls, and modelers should be very careful to avoid them. Many of such difficulties arise from a fundamental (yet often overlooked) property: the so-called structural (or a priori) identifiability, which considers the uniqueness of the estimated parameters. Obviously, the structural identifiability of any tentative model should be checked at the beginning of the model building loop. However, checking this property for arbitrary non-linear dynamic models is not an easy task. Here we present a software toolbox, GenSSI (Generating Series for testing Structural Identifiability), which enables non-expert users to carry out such analysis. The toolbox runs under the popular MATLAB environment and is accompanied by detailed documentation and relevant examples. Availability: The GenSSI toolbox and the related documentation are available at http://www.iim.csic.es/%7Egenssi. Contact: ebalsa@iim.csic.es

Chis, Oana; Banga, Julio R.; Balsa-Canto, Eva

2011-01-01

163

Characterization of autosomal copy-number variation in African Americans: the HyperGEN Study.  

PubMed

African Americans are a genetically diverse population with a high burden of many, common heritable diseases. However, our understanding of genetic variation in African Americans is substandard because of a lack of published population-based genetic studies. We report the distribution of copy-number variation (CNV) in African Americans collected as part of the Hypertension Genetic Epidemiology Network (HyperGEN) using the Affymetrix 6.0 array and the CNV calling algorithms Birdsuite and PennCNV. We present population estimates of CNV from 446 unrelated African-American subjects randomly selected from the 451 families collected within HyperGEN. Although the majority of CNVs discovered were individually rare, we found the frequency of CNVs to be collectively high. We identified a total of 11?070 CNVs greater than 10?kb passing quality control criteria that were called by both algorithms - leading to an average of 24.8 CNVs per person covering 2214?kb (median). We identified 1541 unique copy-number variable regions, 309 of which did not overlap with the Database of Genomic Variants. These results provide further insight into the distribution of CNV in African Americans. PMID:21673747

Wineinger, Nathan E; Pajewski, Nicholas M; Kennedy, Richard E; Wojczynski, Mary K; Vaughan, Laura K; Hunt, Steven C; Gu, C Charles; Rao, Dabeeru C; Lorier, Rachel; Broeckel, Ulrich; Arnett, Donna K; Tiwari, Hemant K

2011-12-01

164

Advanced Technology Development Program for Lithium-Ion Batteries: Gen 2 Performance Evaluation Final Report  

SciTech Connect

The Advanced Technology Development Program has completed performance testing of the second generation of lithium-ion cells (i.e., Gen 2 cells). The 18650-size Gen 2 cells, with a baseline and variant chemistry, were distributed over a matrix consisting of three states-of-charge (SOCs) (60, 80, and 100% SOC), four temperatures (25, 35, 45, and 55°C), and three life tests (calendar-, cycle-, and accelerated-life). The calendar- and accelerated-life cells were clamped at an open-circuit voltage corresponding to the designated SOC and were subjected to a once-per-day pulse profile. The cycle-life cells were continuously pulsed using a profile that was centered around 60% SOC. Life testing was interrupted every four weeks for reference performance tests (RPTs), which were used to quantify changes in cell degradation as a function of aging. The RPTs generally consisted of C1/1 and C1/25 static capacity tests, a low-current hybrid pulse power characterization test, and electrochemical impedance spectroscopy. The rate of cell degradation generally increased with increasing test temperature, and SOC. It was also usually slowest for the calendar-life cells and fastest for the accelerated-life cells. Detailed capacity-, power-, and impedance-based performance results are reported.

Jon P. Christophersen; Ira Bloom; Edward V. Thomas; Kevin L. Gering; Gary L. Henriksen; Vincent S. Battaglia; David Howell

2006-07-01

165

GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees  

PubMed Central

Background A number of software packages are available to generate DNA multiple sequence alignments (MSAs) evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the DNA MSA directly from the transition matrices do not exist. Moreover, existing software restricts to the time-reversible models and it is not optimized to generate nonhomogeneous data (i.e. placing distinct substitution rates at different lineages). Results We present the first package designed to generate MSAs evolving under discrete-time Markov processes on phylogenetic trees, directly from probability substitution matrices. Based on the input model and a phylogenetic tree in the Newick format (with branch lengths measured as the expected number of substitutions per site), the algorithm produces DNA alignments of desired length. GenNon-h is publicly available for download. Conclusion The software presented here is an efficient tool to generate DNA MSAs on a given phylogenetic tree. GenNon-h provides the user with the nonstationary or nonhomogeneous phylogenetic data that is well suited for testing complex biological hypotheses, exploring the limits of the reconstruction algorithms and their robustness to such models.

2012-01-01

166

Advanced Technology Development Program for Lithium-Ion Batteries: Gen 2 GDR Performance Evaluation Report  

SciTech Connect

The Advanced Technology Development Program has completed the performance evaluation of the second generation of lithium-ion cells (i.e., Gen 2 cells). This report documents the testing and analysis of the Gen 2 GDR cells, which were used to learn and debug the newly developed Technology Life Verification Test Manual. The purpose of the manual is to project a 15-year, 150,000 mile battery life capability with a 90% confidence interval using predictive models and short-term testing. The GDR cells were divided into two different matrices. The core-life test matrix consisted of calendar- and cycle-life cells with various changes to the four major acceleration factors (temperature, state-of-charge, throughput, and power rating). The supplemental-life test matrix consisted of cells subjected either to a path dependence study, or a comparison between the standard hybrid pulse power characterization test and the newly-developed minimum pulse power characterization test. Resistance and capacity results are reported.

Jon P. Christophersen; Chinh D. Ho; Gary L. Henriksen; David Howell

2006-07-01

167

pyGenClean: efficient tool for genetic data clean up before association testing  

PubMed Central

Summary: Genetic association studies making use of high-throughput genotyping arrays need to process large amounts of data in the order of millions of markers per experiment. The first step of any analysis with genotyping arrays is typically the conduct of a thorough data clean up and quality control to remove poor quality genotypes and generate metrics to inform and select individuals for downstream statistical analysis. We have developed pyGenClean, a bioinformatics tool to facilitate and standardize the genetic data clean up pipeline with genotyping array data. In conjunction with a source batch-queuing system, the tool minimizes data manipulation errors, accelerates the completion of the data clean up process and provides informative plots and metrics to guide decision making for statistical analysis. Availability and implementation: pyGenClean is an open source Python 2.7 software and is freely available, along with documentation and examples, from http://www.statgen.org. Contact: louis-philippe.lemieux.perreault@umontreal.ca or marie-pierre.dube@statgen.org

Lemieux Perreault, Louis-Philippe; Provost, Sylvie; Legault, Marc-Andre; Barhdadi, Amina; Dube, Marie-Pierre

2013-01-01

168

Flight Deck Technologies to Enable NextGen Low Visibility Surface Operations  

NASA Technical Reports Server (NTRS)

Many key capabilities are being identified to enable Next Generation Air Transportation System (NextGen), including the concept of Equivalent Visual Operations (EVO) . replicating the capacity and safety of today.s visual flight rules (VFR) in all-weather conditions. NASA is striving to develop the technologies and knowledge to enable EVO and to extend EVO towards a Better-Than-Visual operational concept. This operational concept envisions an .equivalent visual. paradigm where an electronic means provides sufficient visual references of the external world and other required flight references on flight deck displays that enable Visual Flight Rules (VFR)-like operational tempos while maintaining and improving safety of VFR while using VFR-like procedures in all-weather conditions. The Langley Research Center (LaRC) has recently completed preliminary research on flight deck technologies for low visibility surface operations. The work assessed the potential of enhanced vision and airport moving map displays to achieve equivalent levels of safety and performance to existing low visibility operational requirements. The work has the potential to better enable NextGen by perhaps providing an operational credit for conducting safe low visibility surface operations by use of the flight deck technologies.

Prinzel, Lawrence (Lance) J., III; Arthur, Jarvis (Trey) J.; Kramer, Lynda J.; Norman, Robert M.; Bailey, Randall E.; Jones, Denise R.; Karwac, Jerry R., Jr.; Shelton, Kevin J.; Ellis, Kyle K. E.

2013-01-01

169

Evaluation of Mixed-Mode Data-Link Communications for NextGen 4DT and Equivalent Visual Surface Operations  

NASA Technical Reports Server (NTRS)

By 2025, U.S. air traffic is predicted to increase 3-fold and may strain the current air traffic management system, which may not be able to accommodate this growth. In response to this challenge, a revolutionary new concept has been proposed for U.S. aviation operations, termed the Next Generation Air Transportation System or NextGen. Many key capabilities are being identified to enable NextGen, including the use of data-link communications. Because NextGen represents a radically different approach to air traffic management and requires a dramatic shift in the tasks, roles, and responsibilities for the flight deck, there are numerous research issues and challenges that must be overcome to ensure a safe, sustainable air transportation system. Flight deck display and crew-vehicle interaction concepts are being developed that proactively investigate and overcome potential technology and safety barriers that might otherwise constrain the full realization of NextGen. The paper describes simulation research examining data-link communications during 4DT and equivalent visual surface operations.

Prinzel, Lawrence J., III; Shelton, Kevin J.; Jones, Denise R.; Allamandola, Angela S.; Arthur, Jarvis, J., III; Bailey, Randall E.

2010-01-01

170

Plant MetGenMAP: An Integrative Analysis System for Plant Systems Biology1[W][OA  

PubMed Central

The information and resources generated from diverse “omics” technologies provide opportunities for producing novel biological knowledge. It is essential to integrate various kinds of biological information and large-scale omics data sets through systematic analysis in order to describe and understand complex biological phenomena. For this purpose, we have developed a Web-based system, Plant MetGenMAP, which can comprehensively integrate and analyze large-scale gene expression and metabolite profile data sets along with diverse biological information. Using this system, significantly altered biochemical pathways and biological processes under given conditions can be retrieved rapidly and efficiently, and transcriptional events and/or metabolic changes in a pathway can be easily visualized. In addition, the system provides a unique function that can identify candidate promoter motifs associated with the regulation of specific biochemical pathways. We demonstrate the functions and application of the system using data sets from Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum), respectively. The results obtained by Plant MetGenMAP can aid in a better understanding of the mechanisms that underlie interesting biological phenomena and provide novel insights into the biochemical changes associated with them at the gene and metabolite levels. Plant MetGenMAP is freely available at http://bioinfo.bti.cornell.edu/tool/MetGenMAP.

Joung, Je-Gun; Corbett, Anthony M.; Fellman, Shanna Moore; Tieman, Denise M.; Klee, Harry J.; Giovannoni, James J.; Fei, Zhangjun

2009-01-01

171

First comparative evaluation of leucocyte differential and reticulocyte count between Abbott Cell DYN 3700 and Beckman-Coulter Gen S  

Microsoft Academic Search

Background: The Cell-Dyn 3700 has been launched with the same CBC and flagging per- formance specifications as the Cell-Dyn 3500. The primary goal of our evaluation was to evaluate the new algorithms of its reticulocyte method and the performance capabilities in comparison to our rou- tine analyser (Coulter Gen S). Methods: The WBC differential and reticulocyte counts were evaluated on

H. Vandeputte; D. Darre; F. Leroy; J. Nemmiche; C. Pucalowski

2003-01-01

172

YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps.  

PubMed

Comparative genetic maps are used in examination of genome organization, detection of conserved gene order, and exploration of marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability of users' own genetic mapping between 2 or more map sets. Users' genetic map data and optional gene annotations are uploaded, either publically or privately, as long as they follow our template which is available in several standard file formats. Data is parsed and loaded into MySQL relational database to be displayed and compared against users' genetic maps or other public data available on YouGenMap. With the highly interactive GUIs, all public data on YouGenMap are maps available for visualization, comparison, search, filtration and download. YouGenMap web tool is available on the website (http://conifergdb.miamioh.edu/yougenmap) with the source-code repository at (http://sourceforge.net/projects/yougenmap/?source=directory). PMID:25009553

Batesole, Keith; Wimalanathan, Kokulapalan; Liu, Lin; Zhang, Fan; Echt, Craig S; Liang, Chun

2014-01-01

173

Redesigning Services for the Net-Gen and Beyond: A Holistic Review of Pedagogy, Resource, and Learning Space  

Microsoft Academic Search

Oblinger and Oblinger (2005) described the Net Generation or Net Gen, who have never known life without the Internet. They note the incremental nature of change: “One generation's technology is taken for granted by the next” (p. 2.1). In a world increasingly dominated by technology, the academic library has become a place to learn that is constantly adapting and changing,

Jill Beard; Penny Dale

2008-01-01

174

Rationale and Design of the National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC) Registry  

PubMed Central

Background Although the management of thoracic aortic aneurysms (TAAs) has improved significantly, patients presenting with aortic dissections, rupture or other acute complications of TAAs continue to suffer high rates of morbidity and mortality. Accumulating data have indicated that many TAAs are due to underlying gene mutations. A comprehensive approach to the study of TAAs resulting from genetic mutations is needed to translate this information into advances in treatment. Objective The National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC) was established to provide a biospecimen inventory and bioinformatics infrastructure to enable research to advance the clinical management of genetically-triggered TAAs and related complications. Methods The GenTAC Registry is a longitudinal observational cohort study enrolling patients with conditions related to genetically-induced TAAs from five regional clinical centers in the United States. Results Over 700 subjects with associated clinical histories, physical examinations, imaging data, and biospecimens have been enrolled in the Registry to date. Enrollment is expected to continue until September 2010. Total enrollment of nearly 3,000 subjects is expected. No interim analysis has yet been undertaken. Conclusions GenTAC has been established to facilitate studies by GenTAC investigators and others that will advance multiple scientific frontiers in thoracic aortic disease. Genotypic, proteomic, clinical, and imaging data will be integrated systematically with outcomes data to determine the optimal clinical management of patients suffering from genetically-induced TAAs.

2010-01-01

175

When You Get a Job to Do, Do It. The Airpower Leadership of Lt Gen William H. Tunner.  

National Technical Information Service (NTIS)

This study examines the development and effectiveness of Lt Gen William H. Tunner's leadership during the interwar years, World War II, and early cold war. This thesis draws upon current Air Force leadership doctrine and propose an Air Force Leadership fr...

D. S. Hanson

2008-01-01

176

The Generic Spacecraft Analyst Assistant (GenSAA): A tool for automating spacecraft monitoring with expert systems  

NASA Technical Reports Server (NTRS)

Flight Operations Analysts (FOAs) in the Payload Operations Control Center (POCC) are responsible for monitoring a satellite's health and safety. As satellites become more complex and data rates increase, FOAs are quickly approaching a level of information saturation. The FOAs in the spacecraft control center for the COBE (Cosmic Background Explorer) satellite are currently using a fault isolation expert system named the Communications Link Expert Assistance Resource (CLEAR), to assist in isolating and correcting communications link faults. Due to the success of CLEAR and several other systems in the control center domain, many other monitoring and fault isolation expert systems will likely be developed to support control center operations during the early 1990s. To facilitate the development of these systems, a project was initiated to develop a domain specific tool, named the Generic Spacecraft Analyst Assistant (GenSAA). GenSAA will enable spacecraft analysts to easily build simple real-time expert systems that perform spacecraft monitoring and fault isolation functions. Lessons learned during the development of several expert systems at Goddard, thereby establishing the foundation of GenSAA's objectives and offering insights in how problems may be avoided in future project, are described. This is followed by a description of the capabilities, architecture, and usage of GenSAA along with a discussion of its application to future NASA missions.

Hughes, Peter M.; Luczak, Edward C.

1991-01-01

177

75 FR 80488 - Notice of Cancellation of Environmental Impact Statement for the Proposed NextGen Project Near...  

Federal Register 2010, 2011, 2012, 2013

...Statement for the Proposed NextGen Project Near Selby, Walworth County, SD (DOE/EIS-0401...load, coal-fired generation facility near Selby, Walworth County, South Dakota...load, coal-fired generation facility near Selby, Walworth County, South...

2010-12-22

178

Ferganasaurus verzilini, gen. et sp. nov., a new neosauropod (Dinosauria, Saurischia, Sauropoda) from the Middle Jurassic of Fergana Valley, Kirghizia  

Microsoft Academic Search

A partial sauropod skeleton from the Middle Jurassic (Callovian) Balabansai Formation in Kirghizia, comprising two dorsal and 16 caudal vertebrae, pelvis and limb bones is described and referred to Ferganasaurus verzilini, gen. et sp. nov. The manus is known only from drawings as original material has been lost; foot bones, except the astragalus, are unknown. Ferganasaurus forms an unresolved polytomy

Vladimir R. Alifanov; Alexander O. Averianov

2003-01-01

179

Preliminary Results From High Temperature Scoping Irradiation Experiments Of Selected Gen IV Structural Metallic Materials  

SciTech Connect

The performance of Generation IV reactors as a class will be determined by the behavior of advanced engineering materials. In the case of materials utilized for reactor internals and pressure vessels, the effects of irradiation are major issues. The environmental conditions for most of the Gen IV reactors are generally beyond present day reactor technology, especially as regards the combinations of operating temperatures, reactor coolant characteristics, and neutron spectra. In some of the applications, the conditions lay well beyond advanced research programs in radiation effects on materials. Therefore, new experimental data as well as analytical predictions of expected behavior of candidate materials at conditions for which there are no experimental data will be required. In the Gen IV Materials Program cross-cutting task, plans are being developed and irradiations and testing are being carried out to address the issues described above. This paper provides preliminary results for the first series of scoping irradiation experiments with selected metallic alloys, some of which are considered candidate materials for current Gen IV reactor applications, while others are considered as potential future candidate materials. The material classes represented are (1) nickel-base alloys (alloy 800H and Inconel 617; (2) advanced oxide-dispersion strengthened steels (14WT and 14YWT); and (3) commercial ferritic-martensitic steels (9Cr-1MoV). The results presented are from tensile tests using small flat tensile specimens (SS-3) in both the unirradiated and irradiated conditions. Specimens were irradiated in so-called rabbit capsules in the High-Flux Isotope Reactor (HFIR) at temperatures from 550 to 750 C and to irradiation doses from about 1.28 to 1.61 dpa. For the preliminary results from the first phase of this study, the annealed 9Cr-1MoV shows small amounts of irradiation-induced hardening. For the Alloy 800H, however, the hardening resulting from the 580 C irradiation was significant, with increases in yield and ultimate strengths on the order of 50 to 100%. Results from the 660 C irradiation also show hardening, but with extremely low tensile elongations when tested at 700 C. For the ODS 14WT and 14YWT materials, the overall results do not indicate significant effects of irradiation at this relatively low exposure. The Inconel 617 will be tested in the second phase of testing.

Nanstad, Randy K [ORNL; McClintock, David A [ORNL; Hoelzer, David T [ORNL

2007-01-01

180

Typing of 48 autosomal SNPs and amelogenin with GenPlex SNP genotyping system in forensic genetics.  

PubMed

GenPlex (Applied Biosystems) is a new SNP genotyping system based on an initial PCR amplification followed by an oligo ligation assay (OLA). The OLA consists of the hybridization of allele and locus specific oligonucleotides (ASOs and LSOs) to PCR products and posterior ligation of ASOs and LSOs. The ligation products are immobilized to microtitre plates and reporter oligonucleotides (ZipChute probes) are hybridized to the ligation products. ZipChute probes are subsequently eluted and detected using capillary electrophoresis. Applied Biosystems developed the GenPlex SNP genotyping system with amelogenin and 48 of the 52 SNPs used in the 52 SNP-plex assay developed by the SNPforID consortium. The system requires equipment that is usually found in forensic genetic laboratories. The use of a robot for performance of the pipetting steps is highly recommendable. A total of 286 individuals from Denmark, Somalia and Greenland were investigated with GenPlex using a Biomek 3000 (Beckman Coulter) robot. The results were compared to results obtained with an ISO 17025 accredited SNP typing assay based on single base extension (SBE). With the GenPlex SNP genotyping system, full SNP profiles were obtained in 97.6% of the investigations. Perfect concordance was obtained in duplicate investigations and the SNP genotypes obtained with the GenPlex system were concordant with those of the accredited SBE based SNP typing system except for one result in rs901398 in one of 286 individuals most likely due to a mutation 6 bp downstream of the SNP. Reproducible SNP genotypes were obtained from as little as 250 pg of DNA. PMID:19083859

Tomas, Carmen; Stangegaard, Michael; Børsting, Claus; Hansen, Anders Johannes; Morling, Niels

2008-12-01

181

Metulocladosporiella gen. nov. for the causal organism of Cladosporium speckle disease of banana.  

PubMed

Cladosporium musae, a widespread leaf-spotting hyphomycete on Musa spp., is genetically and morphologically distinct from Cladosporium s. str. (Davidiella anamorphs, Mycosphaerellaceae, Dothideales). DNA sequence data derived from the ITS and LSU gene regions of C. musae isolates show that this species is part of a large group of hyphomycetes in the Chaetothyriales with dematiaceous blastoconidia in acropetal chains. Cladosporium adianticola, a foliicolous hyphomycete known from leaf litter in Cuba is also a member of this clade and is closely related to C. musae. A comparison with other genera in the Cladosporium complex revealed that C. musae belongs to a lineage for which no generic name is currently available, and for which the genus Metulocladosporiella gen. nov. is proposed. Two species of Metulocladosporiella are currently known, namely M. musae, which is widely distributed, and M. musicola sp. nov., which is currently known from Africa. PMID:16483752

Crous, Pedro W; Schroers, Hans-Josef; Groenewald, Johannes Z; Braun, Uwe; Schubert, Konstanze

2006-03-01

182

Sandrewia, n. gen., a problematical plant from the Lower Permian of Texas and Kansas  

USGS Publications Warehouse

Sandrewia, n. gen., monotypified by S. texana, n. sp., is a plant from Lower Permian beds of north-central Texas and east-central Kansas. It is characterized by stout axes with spirally disposed, laxly inserted, petiolate leaves; the laminae are broadly flabelliform with coarse, open venation. The leaves are reminiscent of the vojnovskyalean Nephropsis, of the Permian Petchora Basin, U.S.S.R., but biologic relationships are only speculative because of limited material. However, leaf characteristics render Sandrewia easily identifiable. Its presently limited stratigraphic range, along with floristic associations, indicates it may be a useful guide fossil and supports the author's beliefs regarding important times and places in Paleozoic plant evolution. ?? 1975.

Mamay, S. H.

1975-01-01

183

NASA System-Level Design, Analysis and Simulation Tools Research on NextGen  

NASA Technical Reports Server (NTRS)

A review of the research accomplished in 2009 in the System-Level Design, Analysis and Simulation Tools (SLDAST) of the NASA's Airspace Systems Program is presented. This research thrust focuses on the integrated system-level assessment of component level innovations, concepts and technologies of the Next Generation Air Traffic System (NextGen) under research in the ASP program to enable the development of revolutionary improvements and modernization of the National Airspace System. The review includes the accomplishments on baseline research and the advancements on design studies and system-level assessment, including the cluster analysis as an annualization standard of the air traffic in the U.S. National Airspace, and the ACES-Air MIDAS integration for human-in-the-loop analyzes within the NAS air traffic simulation.

Bardina, Jorge

2011-01-01

184

Piscirickettsia salmonis gen. nov., sp. nov., the causative agent of an epizootic disease in salmonid fishes.  

PubMed

A novel intracellular pathogen morphologically similar to the ehrlichiae has been isolated in cell culture and identified as the cause of an epizootic disease of salmonid fish. Like the ehrlichiae, the salmonid pathogen, designated strain LF-89, replicates within membrane-bound cytoplasmic vacuoles in host cells. This agent is the first with characteristics of this type to be isolated from a fish. Analysis of the LF-89 16S rRNA indicated that, unlike the ehrlichiae, LF-89 is a gamma proteobacterium distantly related to Coxiella burnetii and perhaps Wolbachia persica. A new genus and species (Piscirickettsia salmonis gen. nov., sp. nov.) are proposed for this organism, with ATCC(R) VR 1361 as the type strain. PMID:1371057

Fryer, J L; Lannan, C N; Giovannoni, S J; Wood, N D

1992-01-01

185

Investigation of strain relaxation in short-period SimGen superlattices using reciprocal space mapping  

NASA Astrophysics Data System (ADS)

The optoelectronic properties of ultrathin SimGen strained layer superlattices (SLSs) depend strongly on their structural perfection and the strain adjustment of the SLS by a Si1-xGex alloy buffer. We used double crystal and triple axis x-ray diffractometry to characterize the structural properties of short period Si6Ge4 and Si9Ge6 SLSs grown on about 1 micrometers thick step-graded SiGe alloy buffers. As grown SLSs and samples annealed subsequently at 550 degree(s)C, 650 degree(s)C, and 780 degree(s)C for 60 min were investigated, the latter to study effects of post-growth thermal treatments typical for conventional Si device fabrication. Precise strain data were extracted from two-dimensional reciprocal space maps around (004) and (224) reciprocal lattice points. These data were used as refined input parameters for the dynamical simulation of the integrated intensity along the q[004] direction.

Koppensteiner, E.; Hamberger, P.; Bauer, Guenther E.; Kibbel, Horst; Presting, Hartmut; Kasper, Erich; Pesek, Andreas

1993-11-01

186

Multimodal information Management: Evaluation of Auditory and Haptic Cues for NextGen Communication Displays  

NASA Technical Reports Server (NTRS)

Auditory communication displays within the NextGen data link system may use multiple synthetic speech messages replacing traditional ATC and company communications. The design of an interface for selecting amongst multiple incoming messages can impact both performance (time to select, audit and release a message) and preference. Two design factors were evaluated: physical pressure-sensitive switches versus flat panel "virtual switches", and the presence or absence of auditory feedback from switch contact. Performance with stimuli using physical switches was 1.2 s faster than virtual switches (2.0 s vs. 3.2 s); auditory feedback provided a 0.54 s performance advantage (2.33 s vs. 2.87 s). There was no interaction between these variables. Preference data were highly correlated with performance.

Begault, Durand R.; Bittner, Rachel M.; Anderson, Mark R.

2012-01-01

187

Life cycle of Schizochytriodinium calani nov. gen. nov. spec., a dinoflagellate parasitizing copepod eggs  

NASA Astrophysics Data System (ADS)

During the Polarstern-cruise ARK IV/2 June 1987, in the Fram Strait, dinophytes parasitizing copepod eggs were observed. In the laboratory on board, vegetative reproduction was documented and re-infection of Calanus glacialis and C. hyperboreus eggs was experimentally established. During food uptake, a primary cyst produces successively several secondary cysts, all separating immediately after formation from the primary cyst. In every one of these free floating secondary cysts up to 256 dinospores are formed by palintomy. Re-infection only occurred after a “maturation time” of at least 2 days after formation of the dinospores. The life cycle is compared to that of other similar parasitic dinophyte genera: Apodinium Chatton, Chytriodinium Chatton, Dissodinium Klebs in Pascher and Myxodinium Cachon, Cachon & Bouquaheux. As the taxon under discussion does not fit in with any species or genus known so far, it is described as Schizochytriodinium calani nov. gen. nov. spec.

Elbrächter, Malte

1988-09-01

188

Eremonidiopsis aggregata, gen. n., sp. n. from Cuba, the third West Indian Dioptinae (Lepidoptera, Notodontidae).  

PubMed

A new genus and species of Dioptinae (Lepidoptera, Noctuoidea, Notodontidae) is described from Cuba, this being the third taxon of the subfamily known from the West Indies. Eremonidiopsis aggregata, gen. n., sp. n., appears to be closely related to Eremonidia mirifica Rawlins & Miller from Hispaniola among members of the tribe Dioptini. Eremonidiopsis aggregata is known from two localities in the middle and western portions of the northeastern Cuban mountain range, Nipe-Sagua-Baracoa. The species inhabits low elevations (300-400 m) covered by lowland rainforest and sclerophyll rainforest. The six known specimens, all males, were part of small swarms flying near the top of an unidentified tree during the day at both collecting sites. These localities are included within protected areas, the "Pico Cristal" National Park in the West and the "Alexander von Humbolt" National Park in the East. PMID:24146561

Aguila, Rayner Núñez

2013-01-01

189

Massilia timonae gen. nov., sp. nov., isolated from blood of an immunocompromised patient with cerebellar lesions.  

PubMed

A fastidious, slowly growing, strictly aerobic, gram-negative bacterium was isolated from a culture of blood from a 25-year-old man with common variable immunodeficiency. The man had been admitted to hospital with febrile progressive cerebellar ataxia. The use of standard phenotypic schemes did not lead to identification, but sequence analysis demonstrated that the 16S rRNA gene of the isolate was most similar to those of the environmental bacteria Duganella zoogloeoides (formerly Zoogloea ramigera 115) and Telluria mixta. Further characterization of the bacterium by biochemical analysis, electron microscopy, G+C content estimation, and fatty acid analysis demonstrated significant differences between the bacterium and D. zoogloeoides and Telluria species; thus, we propose it as a new taxon with the name Massilia timonae gen. nov., sp. nov. PMID:9738031

La Scola, B; Birtles, R J; Mallet, M N; Raoult, D

1998-10-01

190

Enhanced Vision for All-Weather Operations Under NextGen  

NASA Technical Reports Server (NTRS)

Recent research in Synthetic/Enhanced Vision technology is analyzed with respect to existing Category II/III performance and certification guidance. The goal is to start the development of performance-based vision systems technology requirements to support future all-weather operations and the NextGen goal of Equivalent Visual Operations. This work shows that existing criteria to operate in Category III weather and visibility are not directly applicable since, unlike today, the primary reference for maneuvering the airplane is based on what the pilot sees visually through the "vision system." New criteria are consequently needed. Several possible criteria are discussed, but more importantly, the factors associated with landing system performance using automatic and manual landings are delineated.

Bailey, Randall E.; Kramer, Lynda J.; Williams, Steven P.; Bailey, Randall E.; Kramer, Lynda J.; Williams, Steven P.

2010-01-01

191

Combresomyces cornifer gen. sp. nov., an endophytic peronosporomycete in Lepidodendron from the Carboniferous of central France.  

PubMed

Structurally preserved periderm of the lycophyte Lepidodendron rhodumnense from the Visean (Mississippian) of central France contains a peronosporomycete (Combresomyces cornifer gen. sp. nov.) that occurs in the form of pyriform to subglobose terminal oogonia. On the surface is a conspicuous ornamentation, which may have formed through condensation of a mucilaginous extra-oogonial wall secretion. Some oogonia contain thin-walled spherules, which may represent (walled) oospheres or spores of an endoparasitic fungus (?chytrid), whereas single, large spheres in the interior are interpreted as oospores. Antheridia adpressed to several of the specimens are clavate and paragynous. This discovery sheds light on the morphology and biology of peronosporomycetes in a terrestrial ecosystem some 330My ago. Although the organism occurs exclusively in the periderm of L. rhodumnense, it is not known whether it represents a symptomless endophyte, pathogen, or saprotroph. PMID:18692373

Dotzler, Nora; Krings, Michael; Agerer, Reinhard; Galtier, Jean; Taylor, Thomas N

2008-09-01

192

Tucunarella n. Gen. and other dactylogyrids (Monogenoidea) from cichlid fish (Perciformes) from Peruvian Amazonia.  

PubMed

During parasitological research on cichlid fish from the tributaries of the Amazon River around Iquitos, Peru, the following gill monogenoidean species were found: Tucunarella cichlae n. gen. and n. sp. from Cichla monoculus Spix and Agassiz; Gussevia alioides Kritsky, Thatcher, and Boeger, 1986 from Heros severus Heckel; Gussevia asota Kritsky, Thatcher, and Boeger, 1989 from Astronotus ocellatus (Agassiz); Gussevia disparoides Kritsky, Thatcher, and Boeger, 1986 from H. severus (all new geographical records) and Cichlasoma amazonarum Kullander (new host record); Gussevia longihaptor (Mizelle and Kritsky, 1969) Kritsky, Thatcher, and Boeger, 1986 and Gussevia undulata Kritsky, Thatcher, and Boeger, 1986 from C. monoculus ; Sciadicleithrum satanopercae Yamada, Takemoto, Bellay, and Pavanelli, 2008 from Satanoperca jurupari Heckel; and Sciadicleithrum variabilum (Mizelle and Kritsky, 1969) Kritsky, Thatcher, and Boeger, 1989 from C. amazonarum (new host and geographical records). Tucunarella n. gen. is proposed to accommodate a new species, Tucunarella cichlae , which is its type and only known species in the genus. The new genus is characterized by, besides a very large body size (about 1.5 mm vs. much less than 1 mm in other ancyrocephaline genera in Amazonia), a thickened tegument, 1 pair of eyes, overlapping gonads (testis dorsal to the germarium), nonarticulated male copulatory organ (MCO) and accessory piece, a coiled (counterclockwise) MCO, a dextral vaginal aperture, a haptor armed with 2 pairs of anchors (each with broad base and subequal roots, which are marginally folded), and dorsal and ventral bars and 14 hooks with protruding blunt thumbs and 2 different shapes (slender vs. slightly expanded shanks). Illustrations and data on morphological and biometric variability of individual species from different hosts are provided. The present data provide evidence of a relatively wide host specificity of gill monogenoideans parasitic in South American cichlids. PMID:20557192

Mendoza-Franco, Edgar F; Scholz, T; Rozkosná, P

2010-06-01

193

Measurement of the Neutron Electric Form Factor Gen at 0.67 \\(GeV/c\\)2 via 3He-->\\(e-->,e'n\\)  

NASA Astrophysics Data System (ADS)

We have measured the neutron electric form factor Gen via 3He-->\\(e-->,e'n\\)pp at Q2 = 0.67 \\(GeV/c\\)2 using the 3-spectrometer facility of the A1 Collaboration at the Mainz Microtron and a dedicated neutron detector. High pressure polarized 3He--> gas was used as a target of polarized neutrons. Gen is determined from the ratio of the asymmetries A?/A? measured in quasifree kinematics with the target spin perpendicular and parallel to the momentum transfer. We find Gen = 0.052+/-0.011+/-0.005.

Rohe, D.; Bartsch, P.; Baumann, D.; Becker, J.; Bermuth, J.; Bohinc, K.; Böhm, R.; Buttazzoni, S.; Caprano, T.; Clawiter, N.; Deninger, A.; Derber, S.; Ding, M.; Distler, M.; Ebbes, A.; Ebert, M.; Ewald, I.; Friedrich, J.; Friedrich, J. M.; Geiges, R.; Großmann, T.; Hauger, M.; Heil, W.; Honegger, A.; Jennewein, P.; Jourdan, J.; Kahrau, M.; Klein, A.; Kohl, M.; Krygier, K. W.; Kubon, G.; Liesenfeld, A.; Merkel, H.; Merle, K.; Merle, P.; Mühlbauer, M.; Müller, U.; Neuhausen, R.; Otten, E. W.; Petitjean, Th.; Pospischil, Th.; Potokar, M.; Rosner, G.; Schmieden, H.; Sick, I.; Širca, S.; Surkau, R.; Wagner, A.; Walcher, Th.; Warren, G.; Weis, M.; Wöhrle, H.; Zeier, M.

1999-11-01

194

Measurement of the neutron's electric form factor G(E)(n) via doubly polarized, quasi-elastic scattering at Jefferson Lab  

SciTech Connect

We determined the electric form factor of the neutron GEn via the reaction d(e,e?n)p using a longitudinally polarized electron beam and a frozen, polarized 15ND3 target at Jefferson Lab. The knocked out neutrons were detected in a segmented plastic scintillator in coincidence with the quasi-elastically scattered electrons which were tracked in Hall C's High Momentum Spectrometer. To extract GEn, we compared the experimental beam-target asymmetry with theoretical calculations based on different GEn models. We report the results of the fall 2001 run at Q2=0.5 and 1.0 (GeV/c)2.

Frank Wesselmann

2004-11-01

195

GenBank at Los Alamos: User manual, training guide, and reference manual for the ASCII AWB  

SciTech Connect

The GenBank project at Los Alamos collects nucleotide sequence submissions from the biological research community. This work includes the processing of data received in several different forms as well as maintenance and quality control on those submissions. This manual explains the procedures involved in that work for both Los Alamos GenBank staff and off-site users. The GenBank database stores annotated DNA sequences. This manual contains the procedures for depositing these sequences into the database. There are two ways to do this. Either the sequence arrives at GenBank as a submission and is entered by the database staff or the sequence is directly entered by an off-site user. The Annotator's WorkBench (AWB), which is a database browsing and editing tool, is used in both cases. This manual is for GenBank staff and off-site users of the GenBank database at the Los Alamos National Laboratory. It contains an introduction and tutorials for AWB, as well as procedures for entering sequences either as submissions or as data directly deposited by an off-site user. Instructions for all of these are found in Chapters 2 through 4. The introduction to AWB is in Chapter 2. Instructions for submission handling are in Chapter 3. Instructions for entering sequence information are in Chapter 4. Off-site users should look at section 4.3 for instructions on entering a sequence. In addition, the manual describes various in-house curatorial tasks that are part of maintaining the database, as well as the procedures and conventions for annotating sequences. The procedures for annotation and review are in Chapters 5 and 6. The description of in-house curator's tasks is in Chapter 7. The appendices contain: Annotation conventions, two reference chapters on AWB and other utility programs, a complete list of all the forms, fields, and commands in AWB and descriptions of other (non-AWB) software utilities used by database staff.

Reese, G.C.; Keen, G.M.; Gilna, P.; Cinkosky, M.J.

1993-03-15

196

GenBank at Los Alamos: User manual, training guide, and reference manual for the OPEN LOOK[trademark] AWB  

SciTech Connect

The GenBank project at Los Alamos collects nucleotide sequence submissions from the biological research community. This work includes the processing of data received in several different forms as well as maintenance and quality control on those submissions. This manual explains the procedures involved in that work for both Los Alamos GenBank staff and off-site users. The GenBank database stores annotated DNA sequences. This manual contains the procedures for depositing these sequences into the database. There are two ways to do this. Either the sequence arrives at GenBank as a submission and is entered by the database staff or the sequence is directly entered by an off-site user. The Annotator's WorkBench (AWB), which is a database browsing and editing tool, is used in both cases. This manual is for GenBank staff and off-site users of the GenBank database at the Los Alamos National Laboratory. It contains an introduction and tutorials for AWB, as well as procedures for entering sequences either as submissions or as data directly deposited by an off-site user. Instructions for all of these are found in Chapters 2 through 4. The introduction to AWB is in Chapter 2. Instructions for submission handling are in Chapter 3. Instructions for entering sequence information are in Chapter 4. Off-site users should look at section 4.3 for instructions on entering a sequence. In addition, the manual describes various in-house curatorial tasks that are part of maintaining the database, as well as the procedures and conventions for annotating sequences. The procedures for annotation and review are in Chapters 5 and 6. The description of in-house curator's tasks is in Chapter 7. The appendices contain: Annotation conventions, two reference chapters on AWB and other utility programs, a complete list of all the forms, fields, and commands in AWB and descriptions of other (non-AWB) software utilities used by database staff.

Reese, G.C.; Keen, G.M.; Gilna, P.; Cinkosky, M.J.

1993-03-15

197

The Caenorhabditis elegans Homolog of Gen1/Yen1 Resolvases Links DNA Damage Signaling to DNA Double-Strand Break Repair  

PubMed Central

DNA double-strand breaks (DSBs) can be repaired by homologous recombination (HR), which can involve Holliday junction (HJ) intermediates that are ultimately resolved by nucleolytic enzymes. An N-terminal fragment of human GEN1 has recently been shown to act as a Holliday junction resolvase, but little is known about the role of GEN-1 in vivo. Holliday junction resolution signifies the completion of DNA repair, a step that may be coupled to signaling proteins that regulate cell cycle progression in response to DNA damage. Using forward genetic approaches, we identified a Caenorhabditis elegans dual function DNA double-strand break repair and DNA damage signaling protein orthologous to the human GEN1 Holliday junction resolving enzyme. GEN-1 has biochemical activities related to the human enzyme and facilitates repair of DNA double-strand breaks, but is not essential for DNA double-strand break repair during meiotic recombination. Mutational analysis reveals that the DNA damage-signaling function of GEN-1 is separable from its role in DNA repair. GEN-1 promotes germ cell cycle arrest and apoptosis via a pathway that acts in parallel to the canonical DNA damage response pathway mediated by RPA loading, CHK1 activation, and CEP-1/p53–mediated apoptosis induction. Furthermore, GEN-1 acts redundantly with the 9-1-1 complex to ensure genome stability. Our study suggests that GEN-1 might act as a dual function Holliday junction resolvase that may coordinate DNA damage signaling with a late step in DNA double-strand break repair.

Bailly, Aymeric P.; Alpi, Arno; Lilley, David M. J.; Ahmed, Shawn; Gartner, Anton

2010-01-01

198

The Caenorhabditis elegans homolog of Gen1/Yen1 resolvases links DNA damage signaling to DNA double-strand break repair.  

PubMed

DNA double-strand breaks (DSBs) can be repaired by homologous recombination (HR), which can involve Holliday junction (HJ) intermediates that are ultimately resolved by nucleolytic enzymes. An N-terminal fragment of human GEN1 has recently been shown to act as a Holliday junction resolvase, but little is known about the role of GEN-1 in vivo. Holliday junction resolution signifies the completion of DNA repair, a step that may be coupled to signaling proteins that regulate cell cycle progression in response to DNA damage. Using forward genetic approaches, we identified a Caenorhabditis elegans dual function DNA double-strand break repair and DNA damage signaling protein orthologous to the human GEN1 Holliday junction resolving enzyme. GEN-1 has biochemical activities related to the human enzyme and facilitates repair of DNA double-strand breaks, but is not essential for DNA double-strand break repair during meiotic recombination. Mutational analysis reveals that the DNA damage-signaling function of GEN-1 is separable from its role in DNA repair. GEN-1 promotes germ cell cycle arrest and apoptosis via a pathway that acts in parallel to the canonical DNA damage response pathway mediated by RPA loading, CHK1 activation, and CEP-1/p53-mediated apoptosis induction. Furthermore, GEN-1 acts redundantly with the 9-1-1 complex to ensure genome stability. Our study suggests that GEN-1 might act as a dual function Holliday junction resolvase that may coordinate DNA damage signaling with a late step in DNA double-strand break repair. PMID:20661466

Bailly, Aymeric P; Freeman, Alasdair; Hall, Julie; Déclais, Anne-Cécile; Alpi, Arno; Lilley, David M J; Ahmed, Shawn; Gartner, Anton

2010-07-01

199

A new iguanodontid ( Jinzhousaurus yangi gen. et sp. nov.) from the Yixian Formation of western Liaoning, China  

Microsoft Academic Search

A new iguanodontid,Jinzhousaurus yangi gen. et sp. nov., is erected based on the cranial and dental morphology of a specimen from the Yixian Formation of western\\u000a Liaoning. Although a few primitive characteristics remain,Jinzhousaurus yangi display a number of characteristics similar to those seen in derived iguanodontids. Other interesting characteristics include\\u000a the absence of antorbital fenestra and the frontal excluded from

Xiaolin Wang; Xing Xu

2001-01-01

200

Hammondia hammondi gen. nov., sp.nov., from domestic cats, a new coccidian related to Toxoplasma and Sarcocystis  

Microsoft Academic Search

Summary Hammondia hammondi gen.nov.,sp.nov. (Eimeriorina:Sarcocystidae) is described as an obligate heteroxenous protozoon of domestic cats (final host) and laboratory mice (experimental intermediate host). Oocysts from the final host are infectious only for the intermediate host; and cysts from the intermediate host are infectious only for the final host. Intracellular cysts develop principally in striated muscle of mice that ingest oocysts,

J. K. Frenkel; J. P. Dubey

1975-01-01

201

The Neutron Detector for the Measurement of GE^n at high Q^2 in Hall A  

Microsoft Academic Search

Data collection for an asymmetry measurement of the electric form-factor of the neutron, GE^n, was completed during the spring of 2006 in Hall A at the Thomas Jefferson National Accelerator Facility. To detect the neutron from the quasi- elastic ^3He(e,e' n) reaction, a large neutron detector was constructed with an active frontal area of 11.25 m^2. The techniques of the

Jonathan Miller

2006-01-01

202

The impact of message appeal and message source on Gen Y consumers' attitudes and purchase intentions toward American Apparel  

Microsoft Academic Search

A 3 × 2 experimental design was used to examine the impact of message appeal (fair labor, sex, or a combination of fair labor and sex) and message source (company advertisements or third-party publicity) upon Gen Y consumers' (N = 258) intent to patronize the retailer, American Apparel. Results supported models of hierarchical effects of advertising on patronage intention as well as the inclusion

Ruoh-Nan Yan; Jennifer Paff Ogle; Karen H. Hyllegard

2010-01-01

203

WallGen, Software to Construct Layered Cellulose-Hemicellulose Networks and Predict Their Small Deformation Mechanics1  

PubMed Central

We understand few details about how the arrangement and interactions of cell wall polymers produce the mechanical properties of primary cell walls. Consequently, we cannot quantitatively assess if proposed wall structures are mechanically reasonable or assess the effectiveness of proposed mechanisms to change mechanical properties. As a step to remedying this, we developed WallGen, a Fortran program (available on request) building virtual cellulose-hemicellulose networks by stochastic self-assembly whose mechanical properties can be predicted by finite element analysis. The thousands of mechanical elements in the virtual wall are intended to have one-to-one spatial and mechanical correspondence with their real wall counterparts of cellulose microfibrils and hemicellulose chains. User-defined inputs set the properties of the two polymer types (elastic moduli, dimensions of microfibrils and hemicellulose chains, hemicellulose molecular weight) and their population properties (microfibril alignment and volume fraction, polymer weight percentages in the network). This allows exploration of the mechanical consequences of variations in nanostructure that might occur in vivo and provides estimates of how uncertainties regarding certain inputs will affect WallGen's mechanical predictions. We summarize WallGen's operation and the choice of values for user-defined inputs and show that predicted values for the elastic moduli of multinet walls subject to small displacements overlap measured values. “Design of experiment” methods provide systematic exploration of how changed input values affect mechanical properties and suggest that changing microfibril orientation and/or the number of hemicellulose cross-bridges could change wall mechanical anisotropy.

Kha, Hung; Tuble, Sigrid C.; Kalyanasundaram, Shankar; Williamson, Richard E.

2010-01-01

204

Seleniivibrio woodruffii gen. nov., sp. nov., a selenate- and arsenate-respiring bacterium in the Deferribacteraceae.  

PubMed

A Gram-type-negative, obligately anaerobic, selenate-respiring bacterium, strain S4(T), was isolated from activated sludge of a wastewater treatment plant in New Jersey after enrichment with 10 mM selenate as the sole electron acceptor. In addition to its selenate-respiring capability, strain S4(T) also respired arsenate with acetate as carbon source and electron donor. Fermentative growth was not observed. The optimum growth temperature was 37 °C and optimum pH was pH 7. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain S4(T) is a novel member of the family Deferribacteraceae, with the type strain of Denitrovibrio acetiphilus as its closest cultivated relative, with 91.5?% sequence similarity. The cellular fatty acid profile was composed predominantly of straight-chain fatty acids C14?:?0, C15?:?0, C16?:?0, C17?:?0 and C18?:?0, which distinguishes this organism from its closest relatives. The DNA G+C content was 47.7 mol%. Together, these findings support the conclusion that strain S4(T) represents a novel genus and species, for which the name Seleniivibrio woodruffii gen. nov., sp. nov. is proposed. The type strain of Seleniivibrio woodruffii is S4(T) (?=?DSM 24984(T)?=?ATCC BAA-2290(T)). PMID:23625257

Rauschenbach, Ines; Posternak, Valeriya; Cantarella, Pasquale; McConnell, Jennifer; Starovoytov, Valentin; Häggblom, Max M

2013-10-01

205

Variibacter gotjawalensis gen. nov., sp. nov., isolated from soil of a lava forest.  

PubMed

A novel bacterial strain designated GJW-30(T) was isolated from soil of the lava forest, Gotjawal, located in Aewol, Jeju, Korea. Strain GJW-30(T) was found to be strictly aerobic, Gram-negative and to form pleomorphic, non-motile rods and white colonies on R2A agar. The major fatty acids were identified as C18:1?7c, C16:0 and C17:0, the predominant isoprenoid quinone as Q-10, the polar lipids as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminolipid and an unidentified lipid. The cell-wall sugar pattern of strain GJW-30(T) was found to be composed of glucose, ribose and rhamnose and meso-DAP as the diagnostic diamino acid in the cell-wall peptidoglycan. The DNA G+C content of strain GJW-30(T) is 62.2 mol%. Phylogenetic analysis, based on 16S rRNA gene sequence similarities, showed that strain GJW-30(T) forms a deep branch within the order Rhizobiales, sharing the highest level of sequence homology with Bradyrhizobium oligotrophicum LMG 10732(T) (93.6 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, strain GJW-30(T) is considered to represent a novel genus and species, for which the name Variibacter gotjawalensis gen. nov., sp. nov. (the type strain is GJW-30(T) = KCTC 32391(T) = CECT 8514(T) = LMG 28093(T)) is proposed. PMID:24599521

Kim, Kwang Kyu; Lee, Keun Chul; Eom, Mi Kyung; Kim, Jong-Shik; Kim, Dae-Shin; Ko, Suk-Hyung; Kim, Byung-Hyuk; Lee, Jung-Sook

2014-05-01

206

Leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide  

USGS Publications Warehouse

A marine methylotroph, designated strain MB2T, was isolated for its ability to grow on methyl bromide as a sole carbon and energy source. Methyl chloride and methyl iodide also supported growth, as did methionine and glycine betaine. A limited amount of growth was observed with dimethyl sulfide. Growth was also noted with unidentified components of the complex media marine broth 2216, yeast extract and Casamino acids. No growth was observed on methylated amines, methanol, formate, acetate, glucose or a variety of other substrates. Growth on methyl bromide and methyl iodide resulted in their oxidation to CO2 with stoichiometric release of bromide and iodide, respectively. Strain MB2T exhibited growth optima at NaCl and Mg2+ concentrations similar to that of seawater. Phylogenetic analysis of the 16S rDNA sequence placed this strain in the ??-Proteobacteria in proximity to the genera Ruegeria and Roseobacter. It is proposed that strain MB2T (= ATCC BAA-92T = DSM 14336T) be designated Leisingera methylohalidivorans gen. nov., sp. nov.

Schaefer, J. K.; Goodwin, K. D.; McDonald, I. R.; Murrell, J. C.; Oremland, R. S.

2002-01-01

207

Cosmosperma polyloba gen. et sp. nov., a seed plant from the Upper Devonian of South China.  

PubMed

Seed plants with ovules were abundant in the Late Devonian of Euramerica and they contribute significantly to our understanding of their early history. However, coeval ovules have been scarce in other regions of the world. Specimens of the seed plant Cosmosperma polyloba gen. et sp. nov. Wang et al. were recently obtained from the Upper Devonian (Famennian) Wutong Formation, at Fanwan Village, Changxing County, Zhejiang Province, China. This new seed plant has cupulate ovules, the uniovulate cupules with up to 16 distal segments and with minute spines on the outer surface, synangiate pollen organs bearing six to eight microsporangia fused only at the base, and planate and highly dissected pinnules in alternate arrangement. It differs from other Devonian seed plants mainly in the organization and position of the uniovulate and ornamented cupule, and in the highly dissected pinnules. Cosmosperma Wang et al. represents the first Devonian ovules recovered from China or eastern Asia and further illustrates the diversity of early spermatophytes. As for the Late Devonian seed plants, it is suggested that the pollen organs are synangiate and simple in organization, and the branches and leaves are generally planate. PMID:24965709

Wang, Deming; Liu, Le; Meng, Meicen; Xue, Jinzhuang; Liu, Tuo; Guo, Yun

2014-08-01

208

Halocafeteria seosinensis gen. et sp. nov. (Bicosoecida), a halophilic bacterivorous nanoflagellate isolated from a solar saltern.  

PubMed

Recently, heterotrophic nanoflagellates (HNF) have been reported to actively ingest prokaryotes in high salinity waters. We report the isolation and culture of an HNF from a Korean saltern pond of 300 per thousand salinity. The organism is biflagellated with an acronematic anterior flagellum and never glides on surfaces. The mitochondria have tubular cristae. Neither transitional helix nor spiral fiber were observed in the transition zones of the flagella. The cell has a cytostome supported by an arc of eight microtubules, suggesting that our isolate is a bicosoecid. Our isolate had neither mastigonemes, lorica, body scales, nor cytopharynx and thus could not be placed in any of the presently described bicosoecid genera. Phylogenetic analysis of 18S rRNA gene sequences from stramenopiles confirmed the bicosoecid affinities of our isolate, but did not place it within any established genus or family. Its closest relatives include Caecitellus and Cafeteria. The optimal range of growth temperature was 30-35 degrees C. The isolated HNF grew optimally at 150 per thousand salinity and tolerated up to 363 per thousand salinity, but it failed to grow below 75 per thousand salinity, indicating that it could be a borderline extreme halophile. On the basis of its morphological features and position in 18S rRNA trees we propose a novel genus for our isolate; Halocafeteria, n. gen. The species name Halocafeteria seosinensis sp. nov. is proposed. PMID:16874468

Park, Jong S; Cho, Byung C; Simpson, Alastair G B

2006-12-01

209

Canibacter oris gen. nov., sp. nov., isolated from an infected human wound.  

PubMed

A facultatively anaerobic, Gram-reaction-positive, catalase- and oxidase-negative, rod-shaped bacterium isolated from an infected human wound caused by a dog bite was characterized by phenotypic and molecular genetic methods. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMMIB Q2029717T was a member of the order Micrococcales of the class Actinobacteria, displaying 91.6% to 96% sequence similarity with members of the family Microbacteriaceae. Phylogentic trees generated by different algorithms indicated that the strain forms an independent phylogenetic line of descent that consistently clustered proximal to the base of the genus Leucobacter. Chemical studies revealed the presence of a cell-wall murein based on L-lysine (type B1?), major menaquinone (MK-10) and a DNA G+C content of 56.9 mol%. The distinct phylogenetic position, ribotyping and matrix-assisted laser desorption/ionization time-of-flight MS profiles and the significant phenotypic differences clearly separate strain IMMIB Q2029717T from its nearest phylogenetic neighbour and support its classification as a representative of a novel genus and species, with the suggested name Canibacter oris gen. nov., sp. nov. The type strain is IMMIB Q2029717T (=DSM 27064T=CCUG 64069T). PMID:24510975

Aravena-Román, M; Inglis, T J J; Siering, C; Schumann, P; Yassin, A F

2014-05-01

210

Actibacterium mucosum gen. nov., sp. nov., a marine alphaproteobacterium from Mediterranean seawater.  

PubMed

Strain R46(T), a marine alphaproteobacterium, was isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. It is an aerobic chemo-organotrophic, mesophilic and slightly halophilic organism, with complex ionic requirements. Phylogenetic analyses based on the 16S rRNA and gyrB gene sequences showed that strain R46(T) formed a separate branch within the family Rhodobacteraceae, bearing similarities below 94.7 and 80.3%, respectively, to any other recognized species. It contained Q10 as the predominant isoprenoid quinone and C(18:1)?7c/C(18:1)?6c as the major cellular fatty acid. Phosphatidylglycerol was the only identified polar lipid, although other lipids were also detected. The DNA G+C content of the genomic DNA was 61.3 mol%. On the basis of extensive phenotypic and phylogenetic comparative analysis, it is concluded that the strain represents a novel genus and species, for which the name Actibacterium mucosum gen. nov., sp. nov. is proposed. The type strain of the type species is Actibacterium mucosum R46(T) (?= CECT 7668(T)?= KCTC 23349(T)). PMID:22228661

Lucena, Teresa; Ruvira, María A; Garay, Esperanza; Macián, M Carmen; Arahal, David R; Pujalte, María J

2012-12-01

211

Atopostipes suicloacale gen. nov., sp. nov., isolated from an underground swine manure storage pit.  

PubMed

Phenotypic and molecular genetic studies were performed on an unknown facultative anaerobic, catalase-negative, non-spore-forming, rod-shaped bacterium isolated from a pig manure storage pit. The unknown bacterium was nutritionally fastidious with growth enhanced by the addition of rumen fluid and was phenotypically initially identified as an Eubacterium species. Comparative 16S rRNA gene sequencing studies, however, revealed that the unknown bacterium was phylogenetically distant from Eubacterium limosum (the type species of the genus Eubacterium) and related organisms. Phylogenetically, the unknown species displayed a close association with an uncultured organism from human subgingival plaque and formed an unknown sub-line within a cluster of organisms which includes Alloioccoccus otitis, Alkalibacterium olivoapovliticus, Allofustis seminis, Dolosigranulum pigrum, and related organisms, within the low mol% G+C Gram-positive bacteria. Sequence divergence values of >8% with all known taxonomically recognised taxa, however, clearly indicates the novel bacterium represents a hitherto unknown genus. Based on both phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium from pig manure be classified in a new genus and species, as Atopostipes suicloacale gen. nov., sp. nov. The type strain of Atopostipes suicloacale is PPC79(T)=NRRL 23919(T)=DSM 15692(T). PMID:16701518

Cotta, Michael A; Whitehead, Terence R; Collins, Matthew D; Lawson, Paul A

2004-06-01

212

Lombardia GENS: a collaborative registry for monogenic diseases associated with stroke  

PubMed Central

Summary The Italian region of Lombardy, with its existing stroke centers and high-technology laboratories, provides a favorable context for studying monogenic diseases associated with stroke. The Lombardia GENS project was set up to create a regional network for the diagnosis of six monogenic diseases associated with stroke: CADASIL, Fabry disease, MELAS, familial and sporadic hemiplegic migraine, hereditary cerebral amyloid angiopathy and Marfan syndrome. The network comprises 36 stroke centers and seven high-technology laboratories, performing molecular analysis. In this context, all stroke/TIA patients fulfilling clinical criteria for monogenic diseases are currently being included in an ongoing study. Demographic, clinical and family data and diagnostic criteria are collected using standardized forms. On the basis of stroke incidence in Lombardy and the reported prevalence of the diseases considered, we expect, during the course of the study, to collect datasets and DNA samples from more than 200 stroke patients suspected of having monogenic diseases. This will allow evaluation of the regional burden and better phenotype characterization of monogenic diseases associated with stroke.

Bersano, Anna; Baron, Pierluigi; Lanfranconi, Silvia; Trobia, Nadia; Sterzi, Roberto; Motto, Cristina; Comi, Giancarlo; Sessa, Maria; Martinelli-Boneschi, Filippo; Micieli, Giuseppe; Ferrarese, Carlo; Santoro, Patrizia; Parati, Eugenio; Boncoraglio, Giorgio; Padovani, Alessandro; Pezzini, Alessandro; Candelise, Livia

2012-01-01

213

Marinicola seohaensis gen. nov., sp. nov., isolated from sea water of the Yellow Sea, Korea.  

PubMed

A Gram-negative, non-flagellated, non-spore-forming and rod-shaped bacterial strain, SW-152(T), was isolated from sea water of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. Strain SW-152(T) grew optimally at 30 degrees C and in the presence of 2-3 % (w/v) NaCl. It contained MK-7 as the predominant menaquinone and iso-C(15 : 0) and iso-C(15 : 1) as the major fatty acids. Polar lipids detected in strain SW-152(T) were phosphatidylethanolamine, diphosphatidylglycerol and unidentified lipids. The DNA G+C content was 40.3 mol%. Phylogenetic trees based on 16S rRNA gene sequences exhibited that strain SW-152(T) forms a distinct evolutionary lineage within the Cytophaga-Flavobacterium-Bacteroides (CFB) group. Strain SW-152(T) exhibited low 16S rRNA similarity levels of less than 89.4 % to members belonging to the CFB group. Phenotypic properties of strain SW-152(T) differentiate it from phylogenetically related taxa. On the basis of phenotypic and phylogenetic data, strain SW-152(T) (=KCTC 12312(T)=JCM 12600(T)) was classified in a novel genus and species, Marinicola seohaensis gen. nov., sp. nov. PMID:15774675

Yoon, Jung-Hoon; Kang, So-Jung; Lee, Choong-Hwan; Oh, Tae-Kwang

2005-03-01

214

Liberibacter crescens gen. nov., sp. nov., the first cultured member of the genus Liberibacter.  

PubMed

The Gram-stain-negative, rod-shaped bacterial isolate BT-1(T) is the closest relative to the genus 'Candidatus Liberibacter' cultured to date. BT-1(T) was recovered from the phloem sap of a defoliating mountain papaya in Puerto Rico. The BT-1(T) 16S rRNA gene sequence showed that strain BT-1(T) is most closely related to members of the genus 'Ca. Liberibacter' sharing 94.7?% 16S rRNA gene sequence similarity with 'Ca. Liberibacter americanus' and 'Ca. Liberibacter asiaticus'. Additionally, average nucleotide identity, 16S rRNA gene sequences and conserved protein sequences supported inclusion of the previously described species of the genus 'Ca. Liberibacter' in a genus with BT-1(T). The prominent fatty acids of isolate BT-1(T) were C18?:?1?7c (77.2?%), C16?:?0 OH (4.8?%), C18?:?0 (4.4?%) and C16?:?0 (3.5?%). Both physiological and genomic characteristics support the creation of the genus Liberibacter, as well as the novel species Liberibacter crescens gen. nov., sp. nov. with type strain BT-1(T) (?=?ATCC BAA-2481(T)?=?DSM 26877(T)). PMID:24786353

Fagen, Jennie R; Leonard, Michael T; Coyle, Janelle F; McCullough, Connor M; Davis-Richardson, Austin G; Davis, Michael J; Triplett, Eric W

2014-07-01

215

Genetic and Adverse Health Outcome Associations with Treatment Resistant Hypertension in GenHAT  

PubMed Central

Treatment resistant hypertension (TRH) is defined as uncontrolled hypertension (HTN) despite the use of ?3 antihypertensive medication classes or controlled HTN while treated with ?4 antihypertensive medication classes. Risk factors for TRH include increasing age, diminished kidney function, higher body mass index, diabetes, and African American (AA) race. Importantly, previous studies suggest a genetic role in TRH, although the genetics of TRH are largely understudied. With 2203 treatment resistant cases and 2354 treatment responsive controls (36% AA) from the Genetics of Hypertension Associated Treatment Study (GenHAT), we assessed the association of 78 candidate gene polymorphisms with TRH status using logistic regression. After stratifying by race and adjusting for potential confounders, there were 2 genetic variants in the AGT gene (rs699, rs5051) statistically significantly associated with TRH among white participants. The Met allele of rs699 and the G allele of rs5051 were positively associated with TRH: OR = 1.27?(1.12–1.44), P = 0.0001, and OR = 1.36?(1.20–1.53), P < 0.0001, respectively. There was no similar association among AA participants (race interaction P = 0.0004 for rs699 and P = 0.0001 for rs5051). This research contributes to our understanding of the genetic basis of TRH, and further genetic studies of TRH may help reach the goal of better clinical outcomes for hypertensive patients.

Lynch, Amy I.; Irvin, Marguerite R.; Davis, Barry R.; Ford, Charles E.; Eckfeldt, John H.; Arnett, Donna K.

2013-01-01

216

Agaribacter marinus gen. nov., sp. nov., an agar-degrading bacterium from surface seawater.  

PubMed

A Gram-stain-negative, motile, mesophilic, aerobic, rod-shaped bacterium, strain 8-8(T), was isolated from surface seawater at Muroto, Kochi, Japan. The strain exhibited agar-degrading activity. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family Alteromonadaceae and clustered distantly with members of the genus Glaciecola (?94.0?% similarity). The DNA G+C content was 41.8 mol%. The major fatty acids were C16?:?1?7c and/or iso-C15?:?0 2-OH, C16?:?0 and C18?:?1?7c and the major hydroxy fatty acid was C12?:?0 3-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified polar lipid; lysophosphatidylethanolamine and unidentified polar lipids were found as minor components. The major quinone was Q-8. On the basis of phenotypic, genotypic and chemotaxonomic data, strain 8-8(T) represents a novel species of a new genus, for which the name Agaribacter marinus gen. nov., sp. nov. is proposed. The type strain of Agaribacter marinus is 8-8(T) (?=?NBRC 110023(T)?=?LMG 28167(T)). PMID:24763604

Teramoto, Maki; Nishijima, Miyuki

2014-07-01

217

Bandoniozyma gen. nov., a Genus of Fermentative and Non-Fermentative Tremellaceous Yeast Species  

PubMed Central

Background Independent surveys across the globe led to the proposal of a new basidiomycetous yeast genus within the Bulleromyces clade of the Tremellales, Bandoniozyma gen. nov., with seven new species. Methodology/Principal Findings The species were characterized by multiple methods, including the analysis of D1/D2 and ITS nucleotide sequences, and morphological and physiological/biochemical traits. Most species can ferment glucose, which is an unusual trait among basidiomycetous yeasts. Conclusions/Significance In this study we propose the new yeast genus Bandoniozyma, with seven species Bandoniozyma noutii sp. nov. (type species of genus; CBS 8364T ?=? DBVPG 4489T), Bandoniozyma aquatica sp. nov. (UFMG-DH4.20T ?=? CBS 12527T ?=? ATCC MYA-4876T), Bandoniozyma complexa sp. nov. (CBS 11570T ?=? ATCC MYA-4603T ?=? MA28aT), Bandoniozyma fermentans sp. nov. (CBS 12399T ?=? NU7M71T ?=? BCRC 23267T), Bandoniozyma glucofermentans sp. nov. (CBS 10381T ?=? NRRL Y-48076T ?=? ATCC MYA-4760T ?=? BG 02-7-15-015A-1-1T), Bandoniozyma tunnelae sp. nov. (CBS 8024T ?=? DBVPG 7000T), and Bandoniozyma visegradensis sp. nov. (CBS 12505T ?=? NRRL Y-48783T ?=? NCAIM Y.01952T).

Landell, Melissa Fontes; Crestani, Juliana; Pagnocca, Fernando Carlos; Sette, Lara Duraes; Passarini, Michel Rodrigo Zambrano; Rosa, Carlos Augusto; Brandao, Luciana R.; Pimenta, Raphael S.; Ribeiro, Jose Roberto; Garcia, Karina Marques; Lee, Ching-Fu; Suh, Sung-Oui; Peter, Gabor; Dlauchy, Denes; Fell, Jack W.; Scorzetti, Gloria; Theelen, Bart; Vainstein, Marilene H.

2012-01-01

218

Jhaorihella thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring.  

PubMed

A beige-coloured, gram-staining negative, aerobic, non-motile, moderately thermophilic, rod-shaped bacterium, CC-MHSW-1(T), was isolated on Marine Agar 2216 from a water sample from a coastal hot spring on Green Island (Lutao), located off Taituang, Taiwan. 16S rRNA gene sequence analysis demonstrated that the novel strain shared <94?% sequence similarity with members of the genera Lutimaribacter, Maritimibacter and Oceanicola. Ubiquinone (Q-10) was the major respiratory quinone and C(18?:?1)?7c was the predominant fatty acid. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and unidentified phospholipids and aminolipids. The DNA G+C content of strain CC-MHSW-1(T) was 64.7 mol%. On the basis of 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, strain CC-MHSW-1(T) represents a new genus and species in the family Rhodobacteraceae for which the name Jhaorihella thermophila gen. nov., sp. nov., is proposed. The type strain of the type species is CC-MHSW-1(T) (?=?JCM 15068(T)?=?CCM 7767(T)). PMID:20656808

Rekha, P D; Young, Chiu-Chung; Kämpfer, Peter; Martin, Karin; Arun, A B; Chen, Wen-Ming; Lai, Wei-An; Chao, Jiu-Hsing; Shen, Fo-Ting

2011-07-01

219

Lutimaribacter saemankumensis gen. nov., sp. nov., isolated from a tidal flat of the Yellow Sea.  

PubMed

A Gram-negative, non-motile, rod-shaped bacterial strain, designated SMK-117T, belonging to the Alphaproteobacteria, was isolated from a tidal flat of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain SMK-117T grew optimally at pH 7.0-8.0 and 30 degrees C in the presence of 2 % (w/v) NaCl. Neighbour-joining and maximum-likelihood phylogenetic trees based on 16S rRNA gene sequences showed that strain SMK-117T clustered with Maritimibacter alkaliphilus HTCC2654T, with which it exhibited a sequence similarity of 95.3 %. Strain SMK-117T contained Q-10 as the predominant ubiquinone and C(18 : 1)omega7c and 11-methyl C(18 : 1)omega7c as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and two unidentified phospholipids. The DNA G+C content was 63.5 mol%. Strain SMK-117T was differentiated from members of the genera Maritimibacter and Oceanicola on the basis of differences in the fatty acid and polar lipid profiles. The phenotypic, chemotaxonomic and phylogenetic data indicated that strain SMK-117T represents a novel genus and species, for which the name Lutimaribacter saemankumensis gen. nov., sp. nov. is proposed. The type strain of Lutimaribacter saemankumensis is SMK-117T (=KCTC 22244T =CCUG 55760T). PMID:19126722

Yoon, Jung-Hoon; Kang, So-Jung; Lee, Jung-Sook; Oh, Tae-Kwang

2009-01-01

220

Katatopygia gen. n., a monophyletic branch segregated from Boletina (Diptera, Mycetophilidae)  

PubMed Central

Abstract The genus Katatopygia gen. n. is proposed for the Boletina erythropyga/punctus-group that was first introduced by Garrett (1924, 1925) and currently comprises eight described species. Molecular studies have strongly indicated that this group forms a monophyletic sister-group to a clade consisting of all other Boletina, Coelosia and Gnoriste, and its monophyly is supported by morphological data as well. The new genus includes the following species: Katatopygia antoma (Garrett, 1924), comb. n., Katatopygia antica (Garrett, 1924), comb. n., Katatopygia erythropyga (Holmgren, 1883), comb. n.,Katatopygia hissarica (Zaitzev & Polevoi, 2002), comb. n., Katatopygia magna (Garrett, 1925), comb. n., Katatopygia laticauda (Saigusa, 1968), comb. n., Katatopygia neoerythropyga (Zaitzev & Polevoi, 2002), comb. n. andKatatopygia sahlbergi (Lundström, 1906), comb. n., all transferred from Boletina. Katatopygia sahlbergi is found to be a senior synonym of Boletina punctus Garrett, 1925, syn. n. A phylogeny based on morphological data and using parsimony analysis yielded four most parsimonious trees where the new genus is retrieved as monophyletic with high support. Katatopygia neoerythropyga is found to be the sister-taxon to all other species that form two clades, one with Katatopygia sahlbergi-like species and one with Katatopygia erythropyga-like species. A key to males of Katatopygia is provided.

Martinsson, Svante; Kjaerandsen, Jostein

2012-01-01

221

Kistimonas asteriae gen. nov., sp. nov., a gammaproteobacterium isolated from Asterias amurensis.  

PubMed

A novel marine bacterium, strain KMD 001(T), was isolated from the starfish Asterias amurensis, which inhabits the East Sea of Korea. Strain KMD 001(T) was aerobic, light-yellow pigmented and Gram-stain-negative. Analyses of the 16S rRNA gene sequence revealed that strain KMD 001(T) represents a novel lineage within the class Gammaproteobacteria. Strain KMD 001(T) is closely related to the genera Endozoicomonas and Zooshikella, which belong to the family Hahellaceae and to the order Oceanospirillales. The 16S rRNA gene sequence of strain KMD 001(T) shows similarities of approximately 91.8-94.6 % with the above-mentioned genera. The DNA G+C content of KMD 001(T) is 47.6 mol%. It contains Q-9 as the major isoprenoid quinone. The predominant fatty acids were determined to be anteiso-C(15 : 0), iso-C(15 : 0), iso-C(14 : 0) and iso-C(16 : 0). Strain KMD 001(T) should be assigned to a novel bacterial genus within the class Gammaproteobacteria based on its phylogenetic, chemotaxonomic and phenotypic characteristics. The name Kistimonas asteriae gen. nov., sp. nov. is proposed. The type strain is KMD 001(T) (=KCCM 90076(T) =JCM 15607(T)). PMID:19661507

Choi, Eun Ju; Kwon, Hak Cheol; Sohn, Young Chang; Yang, Hyun Ok

2010-04-01

222

Agaricicola taiwanensis gen. nov., sp. nov., an alphaproteobacterium isolated from the edible mushroom Agaricus blazei.  

PubMed

A Gram-negative, beige-pigmented, aerobic, motile, club-shaped bacterium, designated strain CC-SBABM117(T), was isolated from the stipe of the edible mushroom Agaricus blazei Murrill. 16S rRNA gene sequence analysis demonstrated that the strain shared <93 % similarity with the type strains of species in the genera Pannonibacter, Methylopila, Nesiotobacter and Stappia. The organism was unable to produce acid from carbohydrates, but utilized a number of organic acids and amino acids. Ubiquinone 10 (Q-10) was the major respiratory quinone and C(18 : 1) ? 7c, C(19 : 0) cyclo ? 8c, C(16 : 0) and C(18 : 0) were the predominant fatty acids. The predominant polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain CC-SBABM117(T) was 62.7 mol%. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and physiological data, strain CC-SBABM117(T) is considered to represent a novel species of a new genus, for which the name Agaricicola taiwanensis gen. nov., sp. nov. is proposed. The type strain of Agaricicola taiwanensis is CC-SBABM117(T) (=BCRC 17964(T) =CCM 7684(T)). PMID:19819997

Chu, Jiunn-Nan; Arun, A B; Chen, Wen-Ming; Chou, Jui-Hsing; Shen, Fo-Ting; Rekha, P D; Kämpfer, P; Young, Li-Sen; Lin, Shih-Yao; Young, Chiu-Chung

2010-09-01

223

Tepidicella xavieri gen. nov., sp. nov., a betaproteobacterium isolated from a hot spring runoff.  

PubMed

Strains TU-16T and TU-18, two non-pigmented bacterial isolates with an optimum growth temperature of about 45 degrees C and an optimum pH of about 8.5-9.0, were recovered from the Furnas geothermal area on the Island of São Miguel in the Azores. Phylogenetic analysis of the 16S rRNA gene sequence of these strains indicated that they represent a novel species in a new genus of the phylum Betaproteobacteria. The major fatty acids of strains TU-16T and TU-18 were 16 : 0 and 18 : 1omega7c. Ubiquinone 8 was the major respiratory quinone and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The novel isolates were aerobic; thiosulfate was oxidized to sulfate in the presence of a metabolizable carbon source. The organism assimilated organic acids and amino acids, but did not assimilate carbohydrates or polyols. Based on phylogenetic analyses and physiological and biochemical characteristics, it is proposed that strain TU-16T (=LMG 23030T = CIP 108724T) represents the type strain of a novel species in a new genus, Tepidicella xavieri gen. nov., sp. nov. PMID:16585714

França, Luis; Rainey, Fred A; Nobre, M Fernanda; da Costa, Milton S

2006-04-01

224

Aspromonas composti gen. nov., sp. nov., a novel member of the family Xanthomonadaceae.  

PubMed

Two novel bacteria, strains TR7-09(T) and P2-12-1, were isolated from samples of compost and river sediment, respectively. The strains comprised Gram-negative, motile, non-spore-forming rods, produced creamy white colonies on R2A agar, contained Q-8 as the predominant ubiquinone, contained iso-15 : 0, iso-17 : 0 omega 9c and iso-11 : 0 3-OH as the major fatty acids, and had polar lipid profiles consisting of phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and an unknown phospholipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strains were most closely related to Thermomonas haemolytica DSM 13605(T), Silanimonas lenta KCTC 12236(T) and Xanthomonas campestris LMG 568(T) (with 92.5, 92.0 and 92.0 % sequence similarity, respectively) and formed a separate lineage within the family Xanthomonadaceae. The combined genotypic and phenotypic data supported the conclusion that the strains represent a novel genus and species, for which the name Aspromonas composti gen. nov., sp. nov. is proposed. The type strain is TR7-09(T) (=KCTC 12666(T)=DSM 18010(T)). PMID:17684274

Jin, Long; Kim, Kwang Kyu; Im, Wan-Taek; Yang, Hee-Chan; Lee, Sung-Taik

2007-08-01

225

Geofilum rubicundum gen. nov., sp. nov., isolated from deep subseafloor sediment.  

PubMed

A novel, facultatively anaerobic bacterium (strain JAM-BA0501(T)) was isolated from a deep subseafloor sediment sample at a depth of 247 m below seafloor off the Shimokita Peninsula of Japan in the north-western Pacific Ocean (Site C9001, 1180 m water depth). Cells of strain JAM-BA0501(T) were gram-negative, filamentous, non-spore-forming and motile on solid medium by gliding. Phylogenetic analysis based on the 16S rRNA gene sequence of strain JAM-BA0501(T) indicated a distant relationship to strains representing genera within the order Bacteroidales, such as Alkaliflexus imshenetskii Z-7010(T) (91.1?% similarity), Marinilabilia salmonicolor ATCC 19041(T) (86.2?%) and Anaerophaga thermohalophila Fru22(T) (89.3?%). The new isolate produced isoprenoid quinones with menaquinone MK-7 as the major component, and the predominant fatty acids were iso-C(15?:?0) and anteiso-C(15?:?0). The DNA G+C content of the isolate was 42.9 mol%. Based on its taxonomic distinctiveness, strain JAM-BA0501(T) is considered to represent a novel species of a new genus within the family Marinilabiliaceae, for which the name Geofilum rubicundum gen. nov., sp. nov. is proposed. The type strain of Geofilum rubicundum is JAM-BA0501(T) (?=?JCM 15548(T) ?=?NCIMB 14482(T)). PMID:21705444

Miyazaki, Masayuki; Koide, Osamu; Kobayashi, Tohru; Mori, Kozue; Shimamura, Shigeru; Nunoura, Takuro; Imachi, Hiroyuki; Inagaki, Fumio; Nagahama, Takahiko; Nogi, Yuichi; Deguchi, Shigeru; Takai, Ken

2012-05-01

226

Eoetvoesia caeni gen. nov., sp. nov., isolated from an activated sludge system treating coke plant effluent.  

PubMed

A novel bacterium, PB3-7B(T), was isolated on phenol-supplemented inorganic growth medium from a laboratory-scale wastewater purification system that treated coke plant effluent. 16S rRNA gene sequence analysis revealed that strain PB3-7B(T) belonged to the family Alcaligenaceae and showed the highest pairwise sequence similarity to Parapusillimonas granuli Ch07(T) (97.5?%), Candidimonas bauzanensis BZ59(T) (97.3?%) and Pusillimonas noertemannii BN9(T) (97.2?%). Strain PB3-7B(T) was rod-shaped, motile and oxidase- and catalase-positive. The predominant fatty acids were C16?:?0, C17?:?0 cyclo, C19?:?0 cyclo ?8c and C14?:?0 3-OH, and the major respiratory quinone was Q-8. The G+C content of the genomic DNA of strain PB3-7B(T) was 59.7 mol%. The novel bacterium can be distinguished from closely related type strains based on its urease activity and the capacity for assimilation of glycerol and amygdalin. On the basis of the phenotypic, chemotaxonomic and molecular data, strain PB3-7B(T) is considered to represent a new genus and species, for which the name Eoetvoesia caeni gen. nov., sp. nov. is proposed. The type strain of Eoetvoesia caeni is PB3-7B(T) (?=?DSM 25520(T)?=?NCAIM B 02512(T)). PMID:24585374

Felföldi, Tamás; Vengring, Anita; Kéki, Zsuzsa; Márialigeti, Károly; Schumann, Peter; Tóth, Erika M

2014-06-01

227

A new captorhinid reptile, Gansurhinus qingtoushanensis, gen. et sp. nov., from the Permian of China.  

PubMed

Captorhinids, a clade of Paleozoic reptiles, are represented by a rich fossil record that extends from the Late Carboniferous into the Late Permian. Representatives of this clade dispersed from the equatorial regions of Laurasia into the temperate regions of Pangea during the Middle and Late Permian. This rich fossil record shows that there was an evolutionary trend from faunivorous to omnivorous and herbivorous feeding habits within this clade. The discovery of well-preserved captorhinid materials in the Middle Permian of China allows us to determine that the new taxon, Gansurhinus qingtoushanensis, gen. et sp. nov, is a member of Moradisaurinae, a clade of captorhinids with multiple tooth rows arranged in parallel. The presence of this moradisaurine in the Middle Permian of south central Asia leads us to suggest that paleogeographic changes during the Permian, with part of what is today China becoming a large peninsula of Pangea, allowed these early reptiles as well as other terrestrial vertebrates to extend their geographic ranges to this region of the Late Paleozoic supercontinent. PMID:21484260

Reisz, Robert R; Liu, Jun; Li, Jin-Ling; Müller, Johannes

2011-05-01

228

Lombardia GENS: a collaborative registry for monogenic diseases associated with stroke.  

PubMed

The Italian region of Lombardy, with its existing stroke centers and high-technology laboratories, provides a favorable context for studying monogenic diseases associated with stroke. The Lombardia GENS project was set up to create a regional network for the diagnosis of six monogenic diseases associated with stroke: CADASIL, Fabry disease, MELAS, familial and sporadic hemiplegic migraine, hereditary cerebral amyloid angiopathy and Marfan syndrome. The network comprises 36 stroke centers and seven high-technology laboratories, performing molecular analysis. In this context, all stroke/TIA patients fulfilling clinical criteria for monogenic diseases are currently being included in an ongoing study. Demographic, clinical and family data and diagnostic criteria are collected using standardized forms. On the basis of stroke incidence in Lombardy and the reported prevalence of the diseases considered, we expect, during the course of the study, to collect datasets and DNA samples from more than 200 stroke patients suspected of having monogenic diseases. This will allow evaluation of the regional burden and better phenotype characterization of monogenic diseases associated with stroke. PMID:23158583

Bersano, Anna; Baron, Pierluigi; Lanfranconi, Silvia; Trobia, Nadia; Sterzi, Roberto; Motto, Cristina; Comi, Giancarlo; Sessa, Maria; Martinelli-Boneschi, Filippo; Micieli, Giuseppe; Ferrarese, Carlo; Santoro, Patrizia; Parati, Eugenio; Boncoraglio, Giorgio; Padovani, Alessandro; Pezzini, Alessandro; Candelise, Livia

2012-01-01

229

Aurapex penicillata gen. sp. nov. from native Miconia theaezans and Tibouchina spp. in Colombia.  

PubMed

Conidiomata of a fungus resembling Chrysoporthe cubensis, a serious canker pathogen of Eucalyptus spp. (Myrtaceae, Myrtales) in tropical and subtropical parts of the world, was found on Eucalyptus grandis in Colombia. Fruiting structures of the fungus could be distinguished from those of C. cubensis by their distinctly orange conidiomatal necks. This fungus also was found on several plant species native to Colombia including Tibouchina urvilleana, T. lepidota and Miconia theaezans (Melastomataceae, Myrtales). Morphological comparisons, as well as those based on sequences of the ITS1/ITS2 region of the ribosomal DNA repeat and the beta-tubulin gene, were used to characterize this fungus. Its pathogenicity was assessed on various plants from which it has been collected, either in field or greenhouse trials. Phylogenetic analyses showed that isolates reside in a clade distinct from the four clades accommodating Chrysoporthe, Cryphonectria, Endothia and Rostraureum. Members of this clade are distinguished by the presence of orange conidiomatal necks with black bases and a unique internal stromatal structure. No teleomorph has been found for this fungus, for which we have provided the name Aurapex penicillata gen. sp. nov. A. penicillata produced only small lesions after inoculation on young T. urvilleana, M. theaezans and E. grandis trees and appears not to be a serious pathogen. PMID:16800308

Gryzenhout, Marieka; Myburg, Henrietta; Rodas, Carlos A; Wingfield, Brenda D; Wingfield, Michael J

2006-01-01

230

Kaistella koreensis gen. nov., sp. nov., a novel member of the Chryseobacterium-Bergeyella-Riemerella branch.  

PubMed

Gram-negative, non-spore-forming, rod-shaped, yellow-pigmented bacteria isolated from a freshwater stream in Korea were investigated to determine their taxonomic position. Complete 16S rRNA gene sequence analysis indicated that the organisms should be placed in the Chryseobacterium-Bergeyella-Riemerella branch in the family Flavobacteriaceae. Phylogenetically, the strains were most closely related to Chryseobacterium balustinum ATCC 33487(T) and Chryseobacterium scophthalmum LMG 13028(T) (94.3 and 94.1 % 16S rRNA gene sequence similarity, respectively) and they clustered on a separate well-supported branch. The strains contained menaquinone MK-6 as the predominant respiratory quinone and showed higher G+C contents (41.7 mol%) than other species in the Chryseobacterium-Bergeyella-Riemerella branch and i-C(15 : 0) as a major fatty acid (47-52 %). The phylogenetic distances from any species with validly published names and their phenotypic properties confirmed that the strains constitute a separate species in a new genus, for which the name Kaistella koreensis gen. nov., sp. nov. is proposed (type strain Chj707(T)=KCTC 12107(T)=IAM 15050(T)). PMID:15545478

Kim, Myung Kyum; Im, Wan-Taek; Shin, Yong Kook; Lim, Ju Hyoung; Kim, Sung-Hye; Lee, Byung Chul; Park, Mi-Yeoun; Lee, Ki Young; Lee, Sung-Taik

2004-11-01

231

Asaia bogorensis gen. nov., sp. nov., an unusual acetic acid bacterium in the alpha-Proteobacteria.  

PubMed

Eight Gram-negative, aerobic, rod-shaped and peritrichously flagellated strains were isolated from flowers of the orchid tree (Bauhinia purpurea) and of plumbago (Plumbago auriculata), and from fermented glutinous rice, all collected in Indonesia. The enrichment culture approach for acetic acid bacteria was employed, involving use of sorbitol medium at pH 3.5. All isolates grew well at pH 3.0 and 30 degrees C. They did not oxidize ethanol to acetic acid except for one strain that oxidized ethanol weakly, and 0.35% acetic acid inhibited their growth completely. However, they oxidized acetate and lactate to carbon dioxide and water. The isolates grew well on mannitol agar and on glutamate agar, and assimilated ammonium sulfate for growth on vitamin-free glucose medium. The isolates produced acid from D-glucose, D-fructose, L-sorbose, dulcitol and glycerol. The quinone system was Q-10. DNA base composition ranged from 59.3 to 61.0 mol% G + C. Studies of DNA relatedness showed that the isolates constitute a single species. Phylogenetic analysis based on their 16S rRNA gene sequences indicated that the isolates are located in the acetic acid bacteria lineage, but distant from the genera Acetobacter, Gluconobacter, Acidomonas and Gluconacetobacter. On the basis of the above characteristics, the name Asaia bogorensis gen. nov., sp. nov. is proposed for these isolates. The type strain is isolate 71T (= NRIC 0311T = JCM 10569T). PMID:10758893

Yamada, Y; Katsura, K; Kawasaki, H; Widyastuti, Y; Saono, S; Seki, T; Uchimura, T; Komagata, K

2000-03-01

232

Kozakia baliensis gen. nov., sp. nov., a novel acetic acid bacterium in the alpha-proteobacteria.  

PubMed

Four bacterial strains were isolated from palm brown sugar and ragi collected in Bali and Yogyakarta, Indonesia, by an enrichment culture approach for acetic acid bacteria. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four isolates constituted a cluster separate from the genera Acetobacter, Gluconobacter, Acidomonas, Gluconacetobacter and Asaia with a high bootstrap value in a phylogenetic tree. The isolates had high values of DNA-DNA similarity (78-100%) between one another and low values of the similarity (7-25%) to the type strains of Acetobacter aceti, Gluconobacter oxydans, Gluconacetobacter liquefaciens and Asaia bogorensis. The DNA base composition of the isolates ranged from 56.8 to 57.2 mol% G+C with a range of 0-4 mol%. The major quinone was Q-10. The isolates oxidized acetate and lactate to carbon dioxide and water, but the activity was weak, as with strains of Asaia bogorensis. The isolates differed from Asaia bogorensis strains in phenotypic characteristics. The name Kozakia baliensis gen. nov., sp. nov., is proposed for the four isolates. Strain Yo-3T (= NRIC 0488T = JCM 11301T = IFO 16664T = DSM 14400T) was isolated from palm brown sugar collected in Bali, Indonesia, and was designated as the type strain. PMID:12054243

Lisdiyanti, Puspita; Kawasaki, Hiroko; Widyastuti, Yantyati; Saono, Susono; Seki, Tatsuji; Yamada, Yuzo; Uchimura, Tai; Komagata, Kazuo

2002-05-01

233

Effluviibacter roseus gen. nov., sp. nov., isolated from muddy water, belonging to the family "Flexibacteraceae".  

PubMed

A Gram-negative bacterial isolate (designated SRC-1(T)) was isolated from an occasional drainage system and characterized by a polyphasic approach to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain SRC-1(T) with the family "Flexibacteraceae" of the phylum Bacteroidetes. It showed greatest sequence similarity to Pontibacter actiniarum KMM 6156(T) (95.5 %) followed by Adhaeribacter aquaticus MBRG1.5(T) (89.0 %) and Hymenobacter roseosalivarius DSM 11622(T) (88.9 %), but it differed from these micro-organisms in many phenotypic characteristics. Strain SRC-1(T) was an obligate aerobe and its cells were non-motile, irregular rods. The major fatty acids included mainly unsaturated and hydroxy fatty acids, including 17 : 1 iso I/anteiso B (36.7 %), 15 : 0 iso (15.8 %) and 17 : 0 iso 3-OH (10.3 %), and the DNA G+C content was 59.5 mol%. From the phenotypic and genotypic analyses it was clear that strain SRC-1(T) was quite different from members other genera in the family '"Flexibacteraceae". Therefore we conclude that strain SRC-1(T) represents a novel genus, for which the name Effluviibacter gen. nov., containing a single species Effluviibacter roseus sp. nov., is proposed. The type species of the genus is Effluviibacter roseus, the type strain of which is strain SRC-1(T) (=MTCC 7260(T)=DSM 17521(T)). PMID:16825654

Suresh, K; Mayilraj, S; Chakrabarti, T

2006-07-01

234

Celoporthe dispersa gen. et sp. nov. from native Myrtales in South Africa  

PubMed Central

In a survey for Cryphonectria and Chrysoporthe species on Myrtales in South Africa, a fungus resembling the stem canker pathogen Chrysoporthe austroafricana was collected from native Syzygium cordatum near Tzaneen (Limpopo Province), Heteropyxis canescens near Lydenburg (Mpumalanga Province) and exotic Tibouchina granulosa in Durban (KwaZulu-Natal Province). The fungus was associated with dying branches and stems on S. cordatum, H. canescens and T. granulosa. However, morphological differences were detected between the unknown fungus from these three hosts and known species of Chrysoporthe. The aim of this study was to characterise the fungus using DNA sequence comparisons and morphological features. Pathogenicity tests were also conducted to assess its virulence on Eucalyptus (ZG 14 clones), H. natalensis and T. granulosa. Plants of H. canescens were not available for inoculation. Results showed distinct morphological differences between the unknown fungus and Chrysoporthe spp. Phylogenetic analysis showed that isolates reside in a clade separate from Chrysoporthe and other related genera. Celoporthe dispersa gen. et sp. nov. is, therefore, described to accommodate this fungus. Pathogenicity tests showed that C. dispersa is not pathogenic to H. natalensis, but that it is a potential pathogen of Eucalyptus and Tibouchina spp.

Nakabonge, Grace; Gryzenhout, Marieka; Roux, Jolanda; Wingfield, Brenda D.; Wingfield, Michael J.

2006-01-01

235

The Generic Spacecraft Analyst Assistant (GenSAA): A tool for developing graphical expert systems  

NASA Technical Reports Server (NTRS)

During numerous contacts with a satellite each day, spacecraft analysts must closely monitor real-time data. The analysts must watch for combinations of telemetry parameter values, trends, and other indications that may signify a problem or failure. As the satellites become more complex and the number of data items increases, this task is becoming increasingly difficult for humans to perform at acceptable performance levels. At NASA GSFC, fault-isolation expert systems are in operation supporting this data monitoring task. Based on the lessons learned during these initial efforts in expert system automation, a new domain-specific expert system development tool named the Generic Spacecraft Analyst Assistant (GenSAA) is being developed to facilitate the rapid development and reuse of real-time expert systems to serve as fault-isolation assistants for spacecraft analysts. Although initially domain-specific in nature, this powerful tool will readily support the development of highly graphical expert systems for data monitoring purposes throughout the space and commercial industry.

Hughes, Peter M.

1993-01-01

236

Ewingella americana gen.nov., sp.nov., a new Enterobacteriaceae isolated from clinical specimens.  

PubMed

We propose the name Ewingella gen.nov. for a new group in the Enterobacteriaceae. Ewingella is phenotypically distinct from all other groups of Enterobacteriaceae. The members of this genus are lipase- and deoxyribonuclease-negative; Voges-Proskauer-positive; lysine-, ornithine- and arginine-decarboxylase-negative; anaerogenic; they produce acid from glucose in the presence (and absence) of iodoacetate, but fail to produce acid from L-arabinose, melibiose, raffinose, D-sorbitol or sucrose. DNA-relatedness studies (S1-nuclease method) showed that the 10 Ewingella strains studied form a single DNA-hybridization group which is less than 21% related to other members of the Enterobacteriaceae. This single DNA-hybridization group is named Ewingella americana sp. nov. The type strain of E. americana is CDC 1468-78 (= ATCC 33852 = CIP 8194). Although the 10 strains of E. americana were isolated from clinical sources in the United States, the clinical significance of these organisms is not known. PMID:6847036

Grimont, P A; Farmer, J J; Grimont, F; Asbury, M A; Brenner, D J; Deval, C

1983-01-01

237

GenPhilly: a strategy for improving the sustainability of aging in community initiatives.  

PubMed

GenPhilly is an innovative, replicable model that was developed in Philadelphia, Pennsylvania, to inspire and engage emerging leaders from a variety of disciplines to promote and sustain an aging-in-community agenda. Administrative support is provided by the Area Agency on Aging, Philadelphia Corporation for Aging, yet it was designed by its members to be peer-led. In this way, young professionals in their 20s and 30s can capitalize on popular culture to create unique professional development opportunities and get younger generations thinking about the type of city in which they themselves want to get older. The group has benefited the field of aging by building awareness of aging services in the wider community; facilitating cross-disciplinary learning and innovation around aging issues; stressing the competitive advantage for emerging leaders from all fields to know about aging issues; strengthening the aging network workforce; breaking down stereotypes about working with older adults; and introducing expertise from outside the aging network to benefit older adults. Encouraging the development of similar groups will not only benefit the field of aging, it will assist the next generation of leaders in many fields to plan better for their communities and for themselves. PMID:24266521

Clark, Kate

2014-01-01

238

Pelagodinium gen. nov. and P. béii comb. nov., a dinoflagellate symbiont of planktonic foraminifera.  

PubMed

The taxonomic status of the free-living stage of the dinoflagellate Gymnodinium béii, symbiont of the foraminifer Orbulina universa, was reassessed on the basis of detailed morpho-genetic analyses. Electron microscopy observations revealed previously undescribed morphological features of the cell that are important for species recognition. The presence of a single elongated apical vesicle (EAV) ornamented with a row of small knobs, absent in species of the genus Gymnodinium, calls into question the current taxonomic position of the symbiont. The presence of a type E extraplastidial eyespot, the arrangement of the amphiesmal vesicles in series and the absence of trichocysts confirm the affiliation with other symbiotic dinoflagellates and certain genetically related non-symbiotic genera, all belonging to the order Suessiales. The arrangement of the series of vesicles of the analyzed strain is unique within the Suessiales, and the ultrastructure of the pyrenoid is different from other symbiotic dinoflagellates. A large subunit (LSU) rDNA phylogenetic analysis confirmed that the analyzed pelagic symbiont clusters in an independent, well-supported clade within the Suessiales with other sequences of symbiotic dinoflagellates extracted from planktonic foraminifera. Hence a novel genus, Pelagodinium gen. nov., is erected for this pelagic, symbiotic dinoflagellate, and Gymnodinium béii is reclassified as Pelagodinium béii. PMID:20149979

Siano, Raffaele; Montresor, Marina; Probert, Ian; Not, Fabrice; de Vargas, Colomban

2010-07-01

239

Thermogladius shockii gen. nov., sp. nov., a hyperthermophilic crenarchaeote from Yellowstone National Park, USA.  

PubMed

A hyperthermophilic heterotrophic archaeon (strain WB1) was isolated from a thermal pool in the Washburn hot spring group of Yellowstone National Park, USA. WB1 is a coccus, 0.6-1.2 ?m in diameter, with a tetragonal S-layer, vacuoles, and occasional stalk-like protrusions. Growth is optimal at 84°C (range 64-93°C), pH 5-6 (range 3.5-8.5), and <1 g/l NaCl (range 0-4.6 g/l NaCl). Tests of metabolic properties show the isolate to be a strict anaerobe that ferments complex organic substrates. Phylogenetic analysis of the 16S rRNA gene sequence places WB1 in a clade of previously uncultured Desulfurococcaceae and shows it to have ? 96% 16S rRNA sequence identity to Desulfurococcus mobilis, Staphylothermus marinus, Staphylothermus hellenicus, and Sulfophobococcus zilligii. The 16S rRNA gene contains a large insertion similar to homing endonuclease introns reported in Thermoproteus and Pyrobaculum species. Growth is unaffected by the presence of S(0) or SO(4)(2-), thereby differentiating the isolate from its closest relatives. Based on phylogenetic and physiological differences, it is proposed that isolate WB1 represents the type strain of a novel genus and species within the Desulfurococcaceae, Thermogladius shockii gen. nov., sp. nov. (RIKEN = JCM-16579, ATCC = BAA-1607, Genbank 16S rRNA gene = EU183120). PMID:20978744

Osburn, Magdalena R; Amend, Jan P

2011-01-01

240

AGT M235T Genotype/Anxiety Interaction and Gender in the HyperGEN Study  

PubMed Central

Background Both anxiety and elevated heart rate (HR) have been implicated in the development of hypertension. The HyperGen cohort, consisting of siblings with severe and mild hypertension, an age-matched random sample of persons from the same base populations, and unmedicated adult offspring of the hypertensive siblings (N?=?1,002 men and 987 women), was analyzed for an association of the angiotenisinogen AGTM235T genotype (TT, MT, MM) with an endophenotype, heart rate (HR) in high and low anxious groups. Methodology The interaction of AGTM genotype with anxiety, which has been independently associated with hypertension, was investigated adjusting for age, hypertension status, smoking, alcohol consumption, beta blocker medication, body mass index, physical activity and hours of television viewing (sedentary life style). Principal Findings Although there was no main effect of genotype on HR in men or women, high anxious men with the TT genotype had high HR, whereas high anxious men with the MM genotype had low HR. In women, HR was inversely associated with anxiety but there was no interaction with genotype. Conclusion/Significance The results suggest that high anxiety in men with the TT genotype may increase risk for hypertension whereas the MM genotype may be protective in high anxious men. This type of gene x environment interaction may be one reason why genome wide association studies sometimes fail to replicate. The locus may be important only in combination with certain environmental factors.

Knox, Sarah S.; Guo, Xinxin; Zhang, Yuqing; Weidner, G.; Williams, Scott; Ellison, R. Curtis

2010-01-01

241

Using Game Theoretic Models to Predict Pilot Behavior in NextGen Merging and Landing Scenario  

NASA Technical Reports Server (NTRS)

In this paper, we present an implementation of the Semi Network-Form Game framework to predict pilot behavior in a merging and landing scenario. In this scenario, two aircraft are approaching to a freeze horizon with approximately equal distance when they become aware of each other via an ADS-B communication link that will be available in NextGen airspace. Both pilots want to gain advantage over the other by entering the freeze horizon earlier and obtain the first place in landing. They re-adjust their speed accordingly. However, they cannot simply increase their speed to the maximum allowable values since they are concerned with safety, separation distance, effort, possibility of being vectored-off from landing and possibility of violating speed constraints. We present how to model these concerns and the rest of the system using semi network-from game framework. Using this framework, based on certain assumptions on pilot utility functions and on system configuration, we provide estimates of pilot behavior and overall system evolution in time. We also discuss the possible employment of this modeling tool for airspace design optimization. To support this discussion, we provide a case where we investigate the effect of increasing the merging point speed limit on the commanded speed distribution and on the percentage of vectored aircraft.

Yildiz, Yildiray; Lee, Ritchie; Brat, Guillaume

2012-01-01

242

Tyrannobdella rex N. Gen. N. Sp. and the Evolutionary Origins of Mucosal Leech Infestations  

PubMed Central

Background Leeches have gained a fearsome reputation by feeding externally on blood, often from human hosts. Orificial hirudiniasis is a condition in which a leech enters a body orifice, most often the nasopharyngeal region, but there are many cases of leeches infesting the eyes, urethra, vagina, or rectum. Several leech species particularly in Africa and Asia are well-known for their propensity to afflict humans. Because there has not previously been any data suggesting a close relationship for such geographically disparate species, this unnerving tendency to be invasive has been regarded only as a loathsome oddity and not a unifying character for a group of related organisms. Principal Findings A new genus and species of leech from Perú was found feeding from the nasopharynx of humans. Unlike any other leech previously described, this new taxon has but a single jaw with very large teeth. Phylogenetic analyses of nuclear and mitochondrial genes using parsimony and Bayesian inference demonstrate that the new species belongs among a larger, global clade of leeches, all of which feed from the mucosal surfaces of mammals. Conclusions This new species, found feeding from the upper respiratory tract of humans in Perú, clarifies an expansion of the family Praobdellidae to include the new species Tyrannobdella rex n. gen. n.sp., along with others in the genera Dinobdella, Myxobdella, Praobdella and Pintobdella. Moreover, the results clarify a single evolutionary origin of a group of leeches that specializes on mucous membranes, thus, posing a distinct threat to human health.

Phillips, Anna J.; Arauco-Brown, Renzo; Oceguera-Figueroa, Alejandro; Gomez, Gloria P.; Beltran, Maria; Lai, Yi-Te; Siddall, Mark E.

2010-01-01

243

Investigating contact toxicity of Geranium and Artemisia essential oils on Bemisia tabaci Gen.  

PubMed Central

Objective: Sweet potato whitefly, Bemisia tabaci Gen. (B. tabaci), is one of the most important pests of various greenhouse crops in Iran. Nowadays, chemical insecticides are broadly used for control of the pests that causes risk to consumer's health. For the first time, contact toxicity of Pelargonium roseum Andrews and Artemisia sieberi Besser essential oils on B. tabaci and its possible application against the whitefly was evaluated in 2012. Materials and Methods: Essential oil with concentrations of 2500, 1250, 125, and 12 ppm were used. Infested leaves of greenhouse cucumber were treated by mentioned concentrations. After 24 hours, mortality of B. tabaci was recorded and compared after correcting by Abbot's formula. Results: Results showed that all concentrations of the essential oil could significantly reduce population of B. tabaci compared with the control treatment. Phytotoxicity of the treated leaves were recorded after 24, 48, and 72 hours and compared with the control. Concentrations of 2500, 1250, and 125 ppm caused severe phytotoxicity on greenhouse cucumber leaves and therefore are not suitable for greenhouse application. Phytotoxicity of 12 ppm was relatively low. Conclusions: This data implicated suitable protective effects of the essential oils to the pest infestation. Therefore, essential oils distillated from Geranium and Artemisia could be applied to control B. tabaci in greenhouse cucumber at V/V 12 ppm.

Yarahmadi, Fatemeh; Rajabpour, Ali; Zandi Sohani, Nooshin; Ramezani, Leila

2013-01-01

244

Methods for Estimating Environmental Effects and Constraints on NexGen: High Density Case Study  

NASA Technical Reports Server (NTRS)

This document provides a summary of the current methods developed by Metron Aviation for the estimate of environmental effects and constraints on the Next Generation Air Transportation System (NextGen). This body of work incorporates many of the key elements necessary to achieve such an estimate. Each section contains the background and motivation for the technical elements of the work, a description of the methods used, and possible next steps. The current methods described in this document were selected in an attempt to provide a good balance between accuracy and fairly rapid turn around times to best advance Joint Planning and Development Office (JPDO) System Modeling and Analysis Division (SMAD) objectives while also supporting the needs of the JPDO Environmental Working Group (EWG). In particular this document describes methods applied to support the High Density (HD) Case Study performed during the spring of 2008. A reference day (in 2006) is modeled to describe current system capabilities while the future demand is applied to multiple alternatives to analyze system performance. The major variables in the alternatives are operational/procedural capabilities for airport, terminal, and en route airspace along with projected improvements to airframe, engine and navigational equipment.

Augustine, S.; Ermatinger, C.; Graham, M.; Thompson, T.

2010-01-01

245

Characterization and phylogeny of a novel methanotroph, Methyloglobulus morosus gen. nov., spec. nov.  

PubMed

A novel methanotrophic gammaproteobacterium, strain KoM1, was isolated from the profundal sediment of Lake Constance after initial enrichment in opposing gradients of methane and oxygen. Strain KoM1 grows on methane or methanol as its sole source of carbon and energy. It is a Gram-negative methanotroph, often expressing red pigmentation. Cells are short rods and occur sometimes in pairs or short chains. Strain KoM1 grows preferably at reduced oxygen concentrations (pO2=0.05-0.1bar). It can fix nitrogen, and grows at neutral pH and at temperatures between 4 and 30°C. Phylogenetically, the closest relatives are Methylovulum miyakonense and Methylosoma difficile showing 91% 16S rRNA gene sequence identity. The only respiratory quinone is ubiquinone Q8; the main polar lipids are phosphatidyl ethanolamine and phosphatidyl glycerol. The major cellular fatty acids are summed feature 3 (presumably C16:1?7c) and C16:1?5c, and the G+C content of the DNA is 47.7mol%. Strain KoM1 is described as the type strain of a novel species within a new genus, Methyloglobulus morosus gen. nov., sp. nov. PMID:24685906

Deutzmann, J S; Hoppert, M; Schink, B

2014-05-01

246

Sinibacillus soli gen. nov., sp. nov., a moderately thermotolerant member of the family Bacillaceae.  

PubMed

Two Gram-staining-positive, rod-shaped and endospore-forming bacteria that represent a single species, designated strains GD05(T) and GD051, were isolated from a tropical forest soil and a hot spring sediment, respectively. Cells of both strains were facultatively anaerobic, catalase- and oxidase-positive, and could grow optimally at 50 °C, pH 8.0 and with 1?% (w/v) NaCl. Analysis of the 16S rRNA gene sequence revealed that these two isolates belonged to the family Bacillaceae, but did not show sequence similarities of more than 95?% to members of other related genera. The G+C content of the genomic DNA was 43.7-44.1 mol%. The major cellular fatty acids were anteiso-C15?:?0, iso-C15?:?0, iso-C16?:?0 and anteiso-C17?:?0. The main polar lipids were diphosphatidylglycerol and phosphatidylglycerol, and the major menaquinone was MK-7. The peptidoglycan type was A1? (meso-diaminopimelic acid direct). On the basis of this polyphasic taxonomic analysis, the novel strains represent a novel species of a new genus in the family Bacillaceae, order Bacillales, for which the name Sinibacillus soli gen. nov., sp. nov. is proposed. The type strain is GD05(T) (?=?CCTCC AB 2013105(T)?=?KCTC 33117(T)). PMID:24510979

Yang, Guiqin; Zhou, Shungui

2014-05-01

247

Rehaibacterium terrae gen. nov., sp. nov. isolated from a geothermally heated soil sample.  

PubMed

A thermotolerant, alkalitolerant, Gram-stain-negative and strictly aerobic bacterium, designated strain YIM 77974(T), was isolated from a geothermally heated soil sample collected at Rehai National Park, Tengchong, Yunnan province, south-west China. Cells of the strain were rod-shaped and colonies were light brown and circular. The strain grew in the presence of 0-3?% (w/v) NaCl (optimum, 0-1?%) and at pH 7.0-10.0 (optimum, pH 8.0) and 30-55 °C (optimum, 45 °C). The only quinone was Q-8 and the genomic DNA G+C content was 68.3 mol%. Major fatty acids (>10?%) were iso-C16?:?0, iso-C17?:?0, iso-C15?:?0 and iso-C11?:?0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminophospholipid, three unidentified phospholipids and two unidentified polar lipids. On the basis of the morphological and chemotaxonomic characteristics as well as genotypic data, it is proposed that this strain should be classified as a representative of a novel genus and species, Rehaibacterium terrae gen. nov., sp. nov., in the family Xanthomonadaceae. The type strain is strain YIM 77974(T) (?=?DSM 25897(T)?=?CCTCC AB 2012062(T)). PMID:23771618

Yu, Tian-Tian; Yao, Ji-Cheng; Yin, Yi-Rui; Dong, Lei; Liu, Ruo-Fei; Ming, Hong; Zhou, En-Min; Li, Wen-Jun

2013-11-01

248

Antarctobacter heliothermus gen. nov., sp. nov., a budding bacterium from hypersaline and heliothermal Ekho Lake.  

PubMed

Four Gram-negative, aerobic, pointed and budding bacteria were isolated from various depths of the hypersaline, heliothermal and meromictic Ekho Lake (Vestfold Hills, East Antarctica). The cells contained storage granules and formed rosettes. Daughter cells may be motile. Growth required sodium ions. Nitrate was reduced to nitrite, and dissimilatory reduction of nitrite was possible. DNase and gelatinase were produced. Glutamate was metabolized with and without an additional source of combined nitrogen. The most abundant fatty acid was C18:1; other fatty acids present in lower concentrations were C12:1 3-OH, C16:1, C16:0, C18:0 and C19:0 cyc. The main polar lipids were phosphatidylglycerol and phosphatidylcholine. The DNA base composition was 62.3-62.8 mol% G + C. 16S rDNA sequence comparisons showed the isolates to be phylogenetically related to the genera Sagittula and Roseobacter. Morphological, physiological and genotypic differences to these and distinct characteristics supported the description of a new genus and a new species, Antarctobacter heliothermus gen. nov., sp. nov. The type strain is EL-219T (= DSM 11445T). PMID:9828438

Labrenz, M; Collins, M D; Lawson, P A; Tindall, B J; Braker, G; Hirsch, P

1998-10-01

249

Formosa algae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae.  

PubMed

Four light-yellow-pigmented, Gram-negative, short-rod-shaped, non-motile isolates were obtained from enrichment culture during degradation of the thallus of the brown alga Fucus evanescens. The isolates studied were chemo-organotrophic, alkalitolerant and mesophilic. Polar lipids were analysed and phosphatidylethanolamine was the only phospholipid identified. The predominant cellular fatty acids were 15 : 0, i15 : 0, ai15 : 0, i15 : 1 and 15 : 1(n-6). The DNA G+C contents of the four strains were 34.0-34.4 mol%. The level of DNA relatedness of the four isolates was conspecific (88-98 %), indicating that they belong to the same species. The 16S rDNA sequence of strain KMM 3553(T) was determined. Phylogenetic analysis revealed that KMM 3553(T) formed a distinct phyletic line in the phylum Bacteroidetes, class Flavobacteria in the family Flavobacteriaceae and that, phylogenetically, this strain could be placed almost equidistant from the genera Gelidibacter and Psychroserpens (16S rRNA gene sequence similarities of 94 %). On the basis of significant differences in phenotypic and chemotaxonomic characteristics, it is suggested that the isolates represent a novel species in a new genus; the name Formosa algae gen. nov., sp. nov. is proposed. The type strain is KMM 3553(T) (=CIP 107684(T)). PMID:15143012

Ivanova, Elena P; Alexeeva, Yulia V; Flavier, Sébastien; Wright, Jonathan P; Zhukova, Natalia V; Gorshkova, Natalia M; Mikhailov, Valery V; Nicolau, Dan V; Christen, Richard

2004-05-01

250

ProGenGrid: a grid-enabled platform for bioinformatics.  

PubMed

In this paper we describe the ProGenGrid (Proteomics and Genomics Grid) system, developed at the CACT/ISUFI of the University of Lecce which aims at providing a virtual laboratory where e-scientists can simulate biological experiments, composing existing analysis and visualization tools, monitoring their execution, storing the intermediate and final output and finally, if needed, saving the model of the experiment for updating or reproducing it. The tools that we are considering are software components wrapped as Web Services and composed through a workflow. Since bioinformatics applications need to use high performance machines or a high number of workstations to reduce the computational time, we are exploiting a Grid infrastructure for interconnecting wide-spread tools and hardware resources. As an example, we are considering some algorithms and tools needed for drug design, providing them as services, through easy to use interfaces such as the Web and Web service interfaces built using the open source gSOAP Toolkit, whereas as Grid middleware we are using the Globus Toolkit 3.2, exploiting some protocols such as GSI and GridFTP. PMID:15923721

Aloisio, Giovanni; Cafaro, Massimo; Fiore, Sandro; Mirto, Maria

2005-01-01

251

A new captorhinid reptile, Gansurhinus qingtoushanensis, gen. et sp. nov., from the Permian of China  

NASA Astrophysics Data System (ADS)

Captorhinids, a clade of Paleozoic reptiles, are represented by a rich fossil record that extends from the Late Carboniferous into the Late Permian. Representatives of this clade dispersed from the equatorial regions of Laurasia into the temperate regions of Pangea during the Middle and Late Permian. This rich fossil record shows that there was an evolutionary trend from faunivorous to omnivorous and herbivorous feeding habits within this clade. The discovery of well-preserved captorhinid materials in the Middle Permian of China allows us to determine that the new taxon, Gansurhinus qingtoushanensis, gen. et sp. nov, is a member of Moradisaurinae, a clade of captorhinids with multiple tooth rows arranged in parallel. The presence of this moradisaurine in the Middle Permian of south central Asia leads us to suggest that paleogeographic changes during the Permian, with part of what is today China becoming a large peninsula of Pangea, allowed these early reptiles as well as other terrestrial vertebrates to extend their geographic ranges to this region of the Late Paleozoic supercontinent.

Reisz, Robert R.; Liu, Jun; Li, Jin-Ling; Müller, Johannes

2011-05-01

252

Proposal of Yaniellaceae fam. nov., Yaniella gen. nov. and Sinobaca gen. nov. as replacements for the illegitimate prokaryotic names Yaniaceae Li et al. 2005, Yania Li et al. 2004, emend Li et al. 2005, and Sinococcus Li et al. 2006, respectively.  

PubMed

The prokaryotic generic names Yania Li et al. 2004 and Sinococcus Li et al. 2006 are illegitimate because they are later homonyms of the names Yania Roewer 1919 (Opiliones, Arachnida, Arthropoda, Animalia), Yania Huang 1997 (Lepidoptera: Hesperiidae) and Sinococcus Wu and Zheng 2000 (Homoptera: Coccomorpha) [Principle 2 of the Bacteriological Code (1990 Revision)]. Therefore, new generic names, Yaniella gen. nov. and Sinobaca gen. nov., are proposed for these taxa. In addition, a new family name, Yaniellaceae fam. nov., is proposed to accommodate Yaniella gen. nov. As a result, new combinations are required for the species to replace the illegitimate species names. PMID:18218962

Li, Wen-Jun; Zhi, Xiao-Yang; Euzéby, Jean P

2008-02-01

253

GenSo-EWS: a novel neural-fuzzy based early warning system for predicting bank failures.  

PubMed

Bank failure prediction is an important issue for the regulators of the banking industries. The collapse and failure of a bank could trigger an adverse financial repercussion and generate negative impacts such as a massive bail out cost for the failing bank and loss of confidence from the investors and depositors. Very often, bank failures are due to financial distress. Hence, it is desirable to have an early warning system (EWS) that identifies potential bank failure or high-risk banks through the traits of financial distress. Various traditional statistical models have been employed to study bank failures [J Finance 1 (1975) 21; J Banking Finance 1 (1977) 249; J Banking Finance 10 (1986) 511; J Banking Finance 19 (1995) 1073]. However, these models do not have the capability to identify the characteristics of financial distress and thus function as black boxes. This paper proposes the use of a new neural fuzzy system [Foundations of neuro-fuzzy systems, 1997], namely the Generic Self-organising Fuzzy Neural Network (GenSoFNN) [IEEE Trans Neural Networks 13 (2002c) 1075] based on the compositional rule of inference (CRI) [Commun ACM 37 (1975) 77], as an alternative to predict banking failure. The CRI based GenSoFNN neural fuzzy network, henceforth denoted as GenSoFNN-CRI(S), functions as an EWS and is able to identify the inherent traits of financial distress based on financial covariates (features) derived from publicly available financial statements. The interaction between the selected features is captured in the form of highly intuitive IF-THEN fuzzy rules. Such easily comprehensible rules provide insights into the possible characteristics of financial distress and form the knowledge base for a highly desired EWS that aids bank regulation. The performance of the GenSoFNN-CRI(S) network is subsequently benchmarked against that of the Cox's proportional hazards model [J Banking Finance 10 (1986) 511; J Banking Finance 19 (1995) 1073], the multi-layered perceptron (MLP) and the modified cerebellar model articulation controller (MCMAC) [IEEE Trans Syst Man Cybern: Part B 30 (2000) 491] in predicting bank failures based on a population of 3635 US banks observed over a 21 years period. Three sets of experiments are performed-bank failure classification based on the last available financial record and prediction using financial records one and two years prior to the last available financial statements. The performance of the GenSoFNN-CRI(S) network as a bank failure classification and EWS is encouraging. PMID:15109685

Tung, W L; Quek, C; Cheng, P

2004-05-01

254

Comparison of gentamicin dose estimates derived from manual calculations, the Australian 'Therapeutic Guidelines: Antibiotic' nomogram and the SeBA-GEN and DoseCalc software programs  

PubMed Central

Aim To compare gentamicin dose estimates from four predictive methods. Methods A retrospective study was conducted, comprising patients at Fremantle Hospital who received gentamicin therapy and had at least one gentamicin serum concentration reported. A manual calculation method, the Australian ‘Therapeutic Guidelines: Antibiotic’ (TGA) nomogram and the SeBA-GEN and DoseCalc software packages were compared. SeBA-GEN dose estimates were regarded as the reference standard. Results There were 64 males and 30 females with mean age of 58 ± 16 years. In patients with moderate renal impairment (CLCr = 30–60 ml min?1; n = 21), mean dose estimates using DoseCalc and the manual calculation method were comparable to SeBA-GEN but the mean TGA nomogram dose (230 mg; 95% confidence interval 179, 281) was significantly lower than SeBA-GEN (286 mg; 261, 311; P = 0.002; one-way RM anova). In patients with mild renal impairment (CLCr = 60–90 ml min?1; n = 48), DoseCalc (392 mg; 367, 427) was comparable to SeBA-GEN (377 mg; 362, 392). Although the manual method (341 mg; 306, 376; P = 0.007) and the TGA nomogram (335 mg; 302, 368; P < 0.001) estimates were significantly lower than SeBA-GEN, the practical difference was modest. Conclusions SeBA-GEN and DoseCalc are generally comparable for estimation of gentamicin doses in patients with renal impairment. The ‘Therapeutic Guidelines: Antibiotic’ nomogram is a valid approach to dosage estimation, but only when used in patients with normal renal function. Simple manual calculations are a suitable alternative in patients with renal impairment.

Mohan, Mitali; Batty, Kevin T; Cooper, Jennifer A; Wojnar-Horton, Richard E; Ilett, Kenneth F

2004-01-01

255

Edaphobacillus lindanitolerans gen. nov., sp. nov., isolated from hexachlorocyclohexane (HCH) contaminated soil.  

PubMed

A Gram-staining-positive, aerobic, cocco-bacilli-shaped, non-motile, non-spore forming, cream colored strain bacterium (strain MNA4(T) ) was isolated from hexachlorocyclohexane (HCH) contaminated soil. Strain MNA4(T) showed the highest 16S rRNA gene sequence similarity of 97.47% with type species of the newly defined genus Bhargavaea cecembensis. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MNA4(T) belonged to a clade represented by Bhargavaea cecembensis, Bacillus beijingensis and Bacillus ginsengi. DNA-DNA hybridization values of the strain MNA4(T) with close relatives were well below the 70% threshold value recommended for delineation of species. The major fatty acids were anteiso C15:0 , anteiso C17:0 , iso C16:0 and iso C15:0 . The strain was found to contain respiratory quinones MK-8, MK-9 and MK-7 in an approximate molar ratio of 85:7:5. Polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol and two unknown phospholipids. The DNA G?+?C content was 55.6 mol%. Peptidoglycan type was A4? (L-Lys - L-Ala - D-Asp). Phylogenetic analysis, fatty acids profile, phenotypic properties and chemotaxonomic data of strain MNA4(T) indicated that it represents a novel species of a novel genus for which the name Edaphobacillus lindanitolerans gen. nov., sp. nov., is proposed. The type strain is MNA4(T) (=CCM 7584(T) ?=?DSM 22424(T) ). PMID:23322487

Lal, Devi; Khan, Fazlurrahman; Gupta, Sanjay Kumar; Schumann, Peter; Lal, Rup

2013-09-01

256

Hydrogenispora ethanolica gen. nov., sp. nov., an anaerobic carbohydrate-fermenting bacterium from anaerobic sludge.  

PubMed

An anaerobic, spore-forming, ethanol-hydrogen-coproducing bacterium, designated LX-BT, was isolated from an anaerobic sludge treating herbicide wastewater. Cells of strain LX-BT were non-motile rods (0.3-0.5×3.0-18.0 µm). Spores were terminal with a bulged sporangium. Growth occurred at 20-50 °C (optimum 37-45 °C), pH 5.0-8.0 (optimum pH 6.0-7.7) and 0-2.5% (w/v) NaCl. The strain could grow fermentatively on glucose, maltose, arabinose, fructose, xylose, ribose, galactose, mannose, raffinose, sucrose, pectin, starch, glycerol, fumarate, tryptone and yeast extract. The major end-products of glucose fermentation were acetate, ethanol and hydrogen. Yeast extract was not required but stimulated growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite, anthraquinone-2,6-disulfonate, fumarate and Fe (III) nitrilotriacetate were not used as terminal electron acceptors. The G+C content of the genomic DNA was 56.1 mol%. The major cellular fatty acids were anteiso-C15:0, iso-C14:0 and C16:0. The most abundant polar lipids of strain LX-BT were diphosphatidylglycerol and phosphatidylglycerol. 16S rRNA gene sequence analysis revealed that it belongs to an as-yet-unidentified taxon at the order- or class-level (OPB54) within the phylum Firmicutes, showing 86.5% sequence similarity to previously described species of the Desulfotomaculum cluster. The name Hydrogenispora ethanolica gen. nov., sp. nov. is proposed to accommodate strain LX-BT (=DSM 25471T=JCM 18117T=CGMCC 1.5175T) as the type strain. PMID:24554637

Liu, Yi; Qiao, Jiang-Tao; Yuan, Xian-Zheng; Guo, Rong-Bo; Qiu, Yan-Ling

2014-05-01

257

Caloribacterium cisternae gen. nov., sp. nov., an anaerobic thermophilic bacterium from an underground gas storage reservoir.  

PubMed

A novel anaerobic, moderately thermophilic bacterium (strain SGL43(T)) was isolated from Severo-Stavropolskoye underground gas storage reservoir (Russia). Cells of strain SGL43(T) were motile straight rods, 0.4 µm in diameter and 2.0-3.0 µm in length. The temperature range for growth was 28-65 °C, with optimum growth at 50 °C. The pH range for growth was 5.5-8.0, with optimum growth at pH 7.0-7.5. Growth of strain SGL43(T) was observed at NaCl concentrations of 0-4.0% (w/v) with optimum growth at 1.0% (w/v) NaCl. Substrates utilized by strain SGL43(T) included peptone, yeast extract, glucose, fructose, maltose, galactose, pyruvate and citrate. Products of glucose or citrate fermentation were acetate, hydrogen and CO(2). Thiosulfate was reduced to sulfide. The DNA G+C content of strain SGL43(T) was 43.1 mol%. 16S rRNA gene sequence analysis revealed that strain SGL43(T) belongs to the order Thermoanaerobacterales (phylum 'Firmicutes'). The closest relative of strain SGL43(T) was Thermoanaerobacterium saccharolyticum (86.2% 16S rRNA gene sequence similarity with the type strain). Based on the data presented here, strain SGL43(T) is considered to represent a novel species of a new genus, for which the name Caloribacterium cisternae gen. nov., sp. nov. is proposed. The type strain of Caloribacterium cisternae, the type species of the genus, is SGL43(T) (=DSM 23830(T)=VKM B-2670(T)). PMID:21856985

Slobodkina, G B; Kolganova, T V; Kostrikina, N A; Bonch-Osmolovskaya, E A; Slobodkin, A I

2012-07-01

258

Petrimonas sulfuriphila gen. nov., sp. nov., a mesophilic fermentative bacterium isolated from a biodegraded oil reservoir.  

PubMed

A mesophilic, anaerobic, fermentative bacterium, strain BN3(T), was isolated from a producing well of a biodegraded oil reservoir in Canada. Cells were Gram-negative, non-motile rods that did not form spores. The temperature range for growth was 15-40 degrees C, with optimum growth at 37-40 degrees C. The strain grew with up 4 % NaCl, with optimum growth in the absence of NaCl. Tryptone was required for growth. Yeast extract and elemental sulfur stimulated growth. Growth was also enhanced during fermentation of glucose, arabinose, galactose, maltose, mannose, rhamnose, lactose, ribose, fructose, sucrose, cellobiose, lactate, mannitol and glycerol. Acetate, hydrogen and CO(2) were produced during glucose fermentation. Elemental sulfur and nitrate were used as electron acceptors and were reduced to sulfide and ammonium, respectively. The G + C content of the genomic DNA was 40.8 mol%. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the strain was a member of the phylum 'Bacteroidetes', distantly related to the genera Bacteroides and Tannerella (similarity values of less than 90 %). The chemotaxonomic data (fatty acids, polar lipids and quinones composition) also indicated that strain BN3(T) could be clearly distinguished from its closest cultivated relatives. This novel organism possesses phenotypic, chemotaxonomic and phylogenetic traits that do not allow its classification as a member of any previously described genus; therefore, it is proposed that this isolate should be described as a member of a novel species of a new genus, Petrimonas gen. nov., of which Petrimonas sulfuriphila sp. nov. is the type species. The type strain is BN3(T) (= DSM 16547(T) = JCM 12565(T)). PMID:15879242

Grabowski, Agnès; Tindall, Brian J; Bardin, Véronique; Blanchet, Denis; Jeanthon, Christian

2005-05-01

259

Neiella marina gen. nov., sp. nov., isolated from the sea cucumber Apostichopus japonicus.  

PubMed

A novel strain, designated J221(T), was isolated from the intestine of a sea cucumber, Apostichopus japonicus, collected from earthen ponds in Qingdao, China. The strain was Gram-negative, oxidase-positive, aerobic, rod-shaped and motile by means of one to several polar flagella. Growth of strain J221(T) was observed at temperatures between 10 and 40 °C with optimum growth between 25 and 28 °C. The pH range for growth was 5.0-9.0 with optimum growth at pH 7.5-8.0. The dominant fatty acids were summed feature 3 (comprising C16?:?1?7c and/or C16?:?1?6c, 29.04?%), C16?:?0 (28.93?%) and C18?:?1?7c (26.15?%). The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. Diphosphatidylglycerol, an unknown aminolipid and an unknown aminophospholipid were present in moderate to minor amounts in the polar lipid profile. Strain J221(T) had Q-8 as the major respiratory quinone. The DNA G+C content of strain J221(T) was 46.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J221(T) is a member of the Gammaproteobacteria. It formed a distinct phyletic line with less than 91?% sequence similarity to any species within previously recognized genera. On the basis of this polyphasic taxonomic study, strain J221(T) should be classified as a representative of a novel species of a new genus, for which the name Neiella marina gen. nov., sp. nov. is proposed. The type strain of Neiella marina is J221(T) (?=?CGMCC 1.10130(T)?=?NRRL B-51319(T)). PMID:22904222

Du, Zong-Jun; Miao, Ting-Ting; Rooney, Alejandro P; Liu, Qian-Qian; Chen, Guan-Jun

2013-05-01

260

Daeguia caeni gen. nov., sp. nov., isolated from sludge of a textile dye works.  

PubMed

A Gram-negative, non-spore-forming, rod-shaped bacterial strain, K107(T), was isolated from sludge collected from a textile dye works in Korea and its taxonomic position was investigated by means of a polyphasic analysis. Strain K107(T) contained Q-10 as the predominant ubiquinone. The major fatty acids (>10% of total fatty acids) were C(18:1)omega7c and C(18:1) 2-OH. The DNA G+C content was 57.0 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain K107(T) was closely related to the genera Mycoplana, Brucella and Ochrobactrum. Strain K107(T) exhibited 16S rRNA gene sequence similarity values of 96.3-97.1% with respect to the type strains of two Mycoplana species and 94.8-96.8% with respect to members of the genera Brucella and Ochrobactrum. A phylogenetic analysis based on recA gene sequences showed that strain K107(T) forms a distinct phylogenetic lineage within the Alphaproteobacteria. The recA gene sequence of strain K107(T) showed similarity values of 84.5% with respect to type strains of Brucella species and values of 77.6-83.1% with respect to members of the genera Pseudochrobactrum, Ochrobactrum and Mycoplana. Strain K107(T) could be differentiated from phylogenetically related genera by differences in phenotypic properties and fatty acid profiles. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain K107(T) represents a novel genus and species, for which the name Daeguia caeni gen. nov., sp. nov. is proposed. The type strain of Daeguia caeni is strain K107(T) (=KCTC 12981(T) =CCUG 54520(T)). PMID:18175704

Yoon, Jung-Hoon; Kang, So-Jung; Park, Sooyeon; Oh, Tae-Kwang

2008-01-01

261

Visual Advantage of Enhanced Flight Vision System During NextGen Flight Test Evaluation  

NASA Technical Reports Server (NTRS)

Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment. Simulation and flight tests were jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA) to evaluate potential safety and operational benefits of SVS/EFVS technologies in low visibility Next Generation Air Transportation System (NextGen) operations. The flight tests were conducted by a team of Honeywell, Gulfstream Aerospace Corporation and NASA personnel with the goal of obtaining pilot-in-the-loop test data for flight validation, verification, and demonstration of selected SVS/EFVS operational and system-level performance capabilities. Nine test flights were flown in Gulfstream's G450 flight test aircraft outfitted with the SVS/EFVS technologies under low visibility instrument meteorological conditions. Evaluation pilots flew 108 approaches in low visibility weather conditions (600 feet to 3600 feet reported visibility) under different obscurants (mist, fog, drizzle fog, frozen fog) and sky cover (broken, overcast). Flight test videos were evaluated at three different altitudes (decision altitude, 100 feet radar altitude, and touchdown) to determine the visual advantage afforded to the pilot using the EFVS/Forward-Looking InfraRed (FLIR) imagery compared to natural vision. Results indicate the EFVS provided a visual advantage of two to three times over that of the out-the-window (OTW) view. The EFVS allowed pilots to view the runway environment, specifically runway lights, before they would be able to OTW with natural vision.

Kramer, Lynda J.; Harrison, Stephanie J.; Bailey, Randall E.; Shelton, Kevin J.; Ellis, Kyle K.

2014-01-01

262

Paraferrimonas sedimenticola gen. nov., sp. nov., a marine bacterium of the family Ferrimonadaceae.  

PubMed

Three strains (Mok-106(T), Mok-142 and Mok-143) were isolated from marine sediment samples collected from the coast of Okinawa Island, Japan. On the basis of 16S rRNA gene sequence comparisons, the isolates were affiliated with the family Ferrimonadaceae; Shewanella denitrificans and Ferrimonas balearica were the closest relatives, having sequence similarities of 93.7 and 93.0 %, respectively. The novel isolates shared high levels of 16S rRNA gene sequence similarity with each other (98.7-99.3 %) and the results of DNA-DNA hybridization indicated that the three strains belong to the same species. The cells were rod-shaped, motile by means of single polar flagellum and formed colonies that produced a rose-coloured pigment within 6 days incubation at 25 degrees C. The isolates grew in the presence of 0.5-4.0 % (w/v) NaCl and at 15-40 degrees C. The major fatty acids were iso-13 : 0, iso-15 : 0, 16 : 0, 18 : 1 omega 7c and summed feature 3 (16 : 1 omega 7c and/or iso-15 : 0 2-OH). Menaquinone-6, menaquinone-7 and ubiquinone-8 were the major quinones and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 50-51 mol%. Phylogenetic and phenotypic analyses of these isolates suggested that they belong to a novel genus and species of the family Ferrimonadaceae, for which the name Paraferrimonas sedimenticola gen. nov., sp. nov. is proposed. The type strain is Mok-106(T) (=NBRC 101628(T)=CIP 109284(T)). PMID:17625182

Khan, Shams Tabrez; Harayama, Shigeaki

2007-07-01

263

Finding genome-transcriptome-phenome association with structured association mapping and visualization in GenAMap.  

PubMed

Despite the success of genome-wide association studies in detecting novel disease variants, we are still far from a complete understanding of the mechanisms through which variants cause disease. Most of previous studies have considered only genome-phenome associations. However, the integration of transcriptome data may help further elucidate the mechanisms through which genetic mutations lead to disease and uncover potential pathways to target for treatment. We present a novel structured association mapping strategy for finding genome-transcriptome-phenome associations when SNP, gene-expression, and phenotype data are available for the same cohort. We do so via a two-step procedure where genome-transcriptome associations are identified by GFlasso, a sparse regression technique presented previously. Transcriptome-phenome associations are then found by a novel proposed method called gGFlasso, which leverages structure inherent in the genes and phenotypic traits. Due to the complex nature of three-way association results, visualization tools can aid in the discovery of causal SNPs and regulatory mechanisms affecting diseases. Using wellgrounded visualization techniques, we have designed new visualizations that filter through large three-way association results to detect interesting SNPs and associated genes and traits. The two-step GFlasso-gGFlasso algorithmic approach and new visualizations are integrated into GenAMap, a visual analytics system for structured association mapping. Results on simulated datasets show that our approach has the potential to increase the sensitivity and specificity of association studies, compared to existing procedures that do not exploit the full structural information of the data. We report results from an analysis on a publically available mouse dataset, showing that identified SNP-gene-trait associations are compatible with known biology. PMID:22174288

Curtis, Ross E; Yin, Junming; Kinnaird, Peter; Xing, Eric P

2012-01-01

264

Revival of the genus Lentzea and proposal for Lechevalieria gen. nov.  

PubMed

The genus Saccharothrix is phylogenetically heterogeneous on the basis of analysis of almost complete 16S rDNA sequences. An evaluation of chemotaxonomic, morphological and physiological properties in the light of the molecular phylogeny data revealed that several species are misclassified. Saccharothrix aerocolonigenes NRRL B-3298T and Saccharothrix flava NRRL B-16131T constitute a lineage distinct from Saccharothrix and separate from Lentzea. The genus Lechevalieria gen. nov. is proposed for these species. Lechevalieria aerocolonigenes comb. nov. is the type species and S. flava is transferred as Lechevalieria flava comb. nov. Although Lentzea albidocapillata, the type species of the genus Lentzea, was transferred recently to the genus Saccharothrix, the revival of Lentzea is clearly supported by molecular phylogenetic and chemotaxonomic data. The description of the revived genus is emended to include galactose, mannose and traces of ribose as diagnostic whole-cell sugars and MK-9(H4) as the principal menaquinone and elimination of tuberculostearic acid as a diagnostic component in the fatty acid profile. Saccharothrix waywayandensis NRRL B-16159T, S. aerocolonigenes NRRL B-16137 and 'Asiosporangium albidum' IFO 16102 are members of the amended genus Lentzea on the basis of phylogenetic and chemotaxonomic properties. S. waywayandensis is transferred to Lentzea as Lentzea waywayandensis comb. nov., while the new species Lentzea californiensis sp. nov. and Lentzea albida sp. nov. are described for S. aerocolonigenes NRRL B-16137 and 'A. albidum' IFO 16102, respectively. Nucleotide signatures in the 16S rDNA sequences are defined that are diagnostic for the genera Lechevalieria, Lentzea and Saccharothrix. PMID:11411672

Labeda, D P; Hatano, K; Kroppenstedt, R M; Tamura, T

2001-05-01

265

Ciceribacter lividus gen. nov., sp. nov., isolated from rhizosphere soil of chick pea (Cicer arietinum L.).  

PubMed

The taxonomic position of strain MSSRFBL1(T), isolated from chickpea rhizosphere soil from Kannivadi, India, was determined. Strain MSSRFBL1(T) formed bluish black colonies, stained Gram-negative and was motile, aerobic, capable of fixing dinitrogen, oxidase-negative and catalase-positive. Q-10 was the major respiratory quinone. Major fatty acids of strain MSSRFBL1(T) were C18?:?1?7c and C19?:?0cyclo?8c. Minor amounts of C18?:?0, C12?:?0, C14?:?0 3-OH, C18?:?0 3-OH, C16?:?0, C16?:?1?6c/C16?:?1?7c, C17?:?0 3-OH and C20?:?1?7c were also present. Polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine and two unidentified glycolipids. Bacteriohopane derivatives (BHD1 and 2), diplopterol, diploptene, bishomohopanediol, adenosylhopane and 2?-methyl bacteriohopanetetrol were the major hopanoids of strain MSSRFBL1(T). The genomic DNA G+C content was 71 mol%. EzTaxon-e-based blast analysis of the 16S rRNA gene indicated the highest similarity of strain MSSRFBL1(T) to Ensifer adhaerens LMG 20216(T) (97.3?%) and other members of the genus Ensifer (<96.9?%) in the family Rhizobiaceae of the class Alphaproteobacteria. However, phylogenetic analysis based on 16S rRNA, recA, thrC and dnaK gene sequences showed distinct out-grouping from the recognized genera of the family Rhizobiaceae. Based on phenotypic, genotypic and chemotaxonomic characters, strain MSSRFBL1(T) represents a novel species in a new genus in the family Rhizobiaceae for which the name Ciceribacter lividus gen. nov., sp. nov. is proposed. The type strain of Ciceribacter lividus is MSSRFBL1(T) (?=?DSM 25528(T)?=?KCTC 32403(T)). PMID:23907221

Kathiravan, R; Jegan, S; Ganga, V; Prabavathy, V R; Tushar, L; Sasikala, Ch; Ramana, Ch V

2013-12-01

266

Rosenbergiella nectarea gen. nov., sp. nov., in the family Enterobacteriaceae, isolated from floral nectar.  

PubMed

Gram-negative, rod-shaped, oxidase-negative, facultatively anaerobic, yellow-orange-pigmented and motile bacterial strains, designated 8N4(T), 9N2 and 10N3, were isolated from flower nectar of Amygdalus communis (almond) and Citrus paradisi (grapefruit). The 16S rRNA gene sequences of the strains shared highest sequence similarity of 97.0?% with that of Phaseolibacter flectens ATCC 12775(T) and lower similarity with sequences from other type strains of genera of the Enterobacteriaceae. A polyphasic approach that included determination of phenotypic properties and phylogenetic analysis based on 16S rRNA, gyrB, rpoB and atpD gene sequences supported the classification of strains 8N4(T), 9N2 and 10N3 within a novel species in a novel genus in the family Enterobacteriaceae. Strain 8N4(T), and the reference strains of the novel species, grew at 4-35 °C (optimum, 28-30 °C), with 0-5.0?% NaCl (optimum, 3?% NaCl) and with 0-60?% sucrose (optimum, 10-25?% sucrose). Their major cellular fatty acids were C16?:?0, C17?:?0 cyclo, C18?:?1?7c and summed feature 3 (C16?:?1?7c and/or iso-C15?:?0 2-OH). The DNA G+C content of strain 8N4(T) was 46.8 mol%. On the basis of phenotypic properties and phylogenetic distinctiveness, the floral nectar isolates are classified within a novel species in a new genus in the family Enterobacteriaceae, for which the name Rosenbergiella nectarea gen. nov., sp. nov. is proposed. The type strain of Rosenbergiella nectarea is 8N4(T) (?=?LMG 26121(T)?=?DSM 24150(T)). PMID:23832968

Halpern, Malka; Fridman, Svetlana; Atamna-Ismaeel, Nof; Izhaki, Ido

2013-11-01

267

Pseudocollinia brintoni gen. nov., sp. nov. (Apostomatida: Colliniidae), a parasitoid ciliate infecting the euphausiid Nyctiphanes simplex.  

PubMed

A novel parasitoid ciliate, Pseudocollinia brintoni gen. nov., sp. nov. was discovered infecting the subtropical sac-spawning euphausiid Nyctiphanes simplex off both coasts of the Baja California peninsula, Mexico. We used microscopic, and genetic information to describe this species throughout most of its life cycle. Pseudocollinia is distinguished from other Colliniidae genera because it exclusively infects euphausiids, has a polymorphic life cycle, and has a small cone-shaped oral cavity whose left wall has a field of ciliated kinetosomes and whose opening is surrounded on the left and right by 2 'oral' kineties (or ciliary rows) that terminate at its anterior border. Two related species that infect different euphausiid species from higher latitudes in the northeastern Pacific Ocean, Collinia beringensis Capriulo and Small, 1986, briefly redescribed herein, and Collinia oregonensis Gómez-Gutiérrez, Peterson, and Morado, 2006, are transferred to the genus Pseudocollinia. P. brintoni has between 12 and 18 somatic kineties, and its oral cavity has only 2 oral kineties, while P. beringensis comb. nov. has more somatic kineties, including 3 oral kineties. P. oregonensis comb. nov. has an intermediate number of somatic kineties. P. beringensis comb. nov. also infects Thysanoessa raschi (a new host species). SSU rRNA and cox1 gene sequences demonstrated that Pseudocollinia ciliates are apostome ciliates and that P. brintoni is different from P. beringensis comb. nov. High densities of rod-shaped bacteria (1.7 µm length, 0.2 to 0.5 µm diameter) were associated with P. brintoni. After euphausiid rupture, high concentrations of P. brintoni and bacteria cluster to form 3 to 6 cm long filaments where tomites encyst and transform to the phoront stage; this is a novel place for encystation. P. brintoni may complete its life cycle when the euphausiids feed on these filaments. PMID:22585303

Gómez-Gutiérrez, J; Strüder-Kypke, M C; Lynn, D H; Shaw, T C; Aguilar-Méndez, M J; López-Cortés, A; Martínez-Gómez, S; Robinson, C J

2012-05-15

268

Sejongia antarctica gen. nov., sp. nov. and Sejongia jeonii sp. nov., isolated from the Antarctic.  

PubMed

Two yellow-pigmented, Gram-negative and aerobic bacterial strains, designated AT1013T and AT1047T, were isolated from terrestrial samples of the Antarctic. On the basis of 16S rRNA gene sequence analyses, the two Antarctic strains shared 97.7 % sequence similarity and showed moderate relationships to the genera Chryseobacterium (92.5-95.3 %), Riemerella (92.3-93.5 %), Bergeyella (92.5-92.6 %) and Kaistella (92.5-93.3 %). In phylogenetic analyses, the two isolates formed a robust monophyletic clade and represented a distinct phyletic line that equated to novel generic status. Cells were non-motile, non-gliding and psychrotolerant with an optimum growth temperature of about 20 degrees C. Flexirubins were absent. The major isoprenoid quinone was MK-6. The predominant cellular fatty acids were 15 : 0 iso, 15 : 0 anteiso and 17 : 1 iso omega9c. DNA G+C contents were 34-36 mol%. The two isolates shared low genomic relatedness (27 %) and were differentiated from each other by several phenotypic characteristics. The polyphasic data presented in this study indicated that these isolates should be recognized as two separate novel species in a novel genus within the family Flavobacteriaceae. The name Sejongia gen. nov. is therefore proposed for the Antarctic isolates, with the type species Sejongia antarctica sp. nov. (type strain AT1013T=IMSNU 14040T=KCTC 12225T=JCM 12381T) and Sejongia jeonii sp. nov. (type strain AT1047T=IMSNU 14049T=KCTC 12226T=JCM 12382T). PMID:15653910

Yi, Hana; Yoon, Ho Il; Chun, Jongsik

2005-01-01

269

Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophile.  

PubMed

The isolation of a new thermophilic bacterium, Thermus aquaticus gen. n. and sp. n., is described. Successful enrichment requires incubation at 70 to 75 C, and the use of nutrient media relatively dilute with respect to the organic components. Strains of T. aquaticus have been isolated from a variety of thermal springs in Yellowstone National Park and from a thermal spring in California. The organism has also been isolated from man-made thermal habitats, such as hot tap water, in geographical locations quite distant from thermal springs. Isolates of T. aquaticus are gram-negative nonsporulating nonmotile rods which frequently form long filaments at supraoptimal temperatures or in the stationary phase. All isolates form a yellow cellular pigment, probably a carotenoid. A characteristic structure formed by all isolates is a large sphere, considerably larger than a spheroplast. These large spheres, as well as lysozyme-induced spheroplasts, are resistant to osmotic lysis. Deoxyribonucleic acid base compositions of four strains were determined by CsCl density gradient ultracentrifugation and found to be between 65.4 and 67.4 moles per cent guanine plus cytosine. The growth of all isolates tested is inhibited by fairly low concentrations of cycloserine, streptomycin, penicillin, novobiocin, tetracycline, and chloramphenicol. Nutritional studies on one strain showed that it did not require vitamins or amino acids, although growth was considerably faster in enriched than in synthetic medium. Several sugars and organic acids served as carbon sources, and either NH(4) (+) or glutamate could serve as nitrogen source. The organism is an obligate aerobe and has a pH optimum of 7.5 to 7.8. The optimum temperature for growth is 70 C, the maximum 79 C, and the minimum about 40 C. The generation time at the optimum is about 50 min. The possible relationships of this new genus to the myxobacteria, flexibacteria, and flavobacteria are discussed. PMID:5781580

Brock, T D; Freeze, H

1969-04-01

270

Falsirhodobacter halotolerans gen. nov., sp. nov., isolated from dry soils of a solar saltern.  

PubMed

Two bacterial strains (JA744(T) and JA745) were isolated from dry soil samples collected from solar salterns at Humma, Odisha, India. Both strains were Gram-stain-negative, catalase- and oxidase-positive, motile rods. Major fatty acids in both strains included C18:1?7c, C18:0 and C16:0, while minor amounts of C10:0 3-OH, C12:0, C12:0 3-OH, C14:0 and C16:0 were also present. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified glycolipid, five unidentified lipids, an unidentified aminolipid and an unidentified phospholipid made up the polar lipids of both strains. Both strains had bacteriohopane derivatives (BHD1,2) and diploptene as major hopanoids. Mean genomic DNA G+C content was 75 ± 1 mol% and the two strains were closely related (mean DNA-DNA hybridization >90%). Phylogenetic analysis based on the 16S rRNA gene sequence showed that the two strains clustered with species of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria. The highest sequence similarity was observed with Rhodobacter sphaeroides ATH2.4.1(T) (96%) and other members of the genera Rhodobacter and Pseudorhodobacter (<96%). However, the two strains were positioned distinctly outside the group formed by the other genera of the family Rhodobacteraceae. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of these isolates as representatives of a novel species in a new genus, for which the name Falsirhodobacter halotolerans gen. nov., sp. nov. is proposed. The type strain of Falsirhodobacter halotolerans is JA744(T) (=KCTC 32158(T) =NBRC 108897(T)). PMID:23104358

Subhash, Y; Tushar, L; Sasikala, Ch; Ramana, Ch V

2013-06-01

271

Ameyamaea chiangmaiensis gen. nov., sp. nov., an acetic acid bacterium in the alpha-Proteobacteria.  

PubMed

Two isolates, AC04(T) and AC05, were isolated from the flowers of red ginger collected in Chiang Mai, Thailand. In phylogenetic trees based on 16S rRNA gene sequences, the two isolates were included within a lineage comprised of the genera Acidomonas, Gluconacetobacter, Asaia, Kozakia, Swaminathania, Neoasaia, Granulibacter, and Tanticharoenia, and they formed an independent cluster along with the type strain of Tanticharoenia sakaeratensis. The calculated pair-wise sequence similarities of isolate AC04(T) were 97.8-92.5% to the type strains of the type species of the 11 genera of acetic acid bacteria. The DNA base composition was 66.0-66.1 mol % G+C with a range of 0.1 mol %. A single-stranded, labeled DNA from isolate AC04(T) presented levels of DNA-DNA hybridization of 100, 85, 4, and 3% respectively to DNAs from isolates AC04(T) and AC05 and the type strains of Tanticharoenia sakaeratensis and Gluconacetobacter liquefaciens. The two isolates were unique morphologically in polar flagellation and physiologically in intense acetate oxidation to carbon dioxide and water and weak lactate oxidation. The intensity in acetate oxidation almost equaled that of the type strain of Acetobacter aceti. The two isolates had Q-10. Isolate AC04(T) was discriminated from the type strains of the type species of the 11 genera by 16S rRNA gene restriction analysis using restriction endonucleases TaqI and Hin6I. The unique phylogenetic, genetic, morphological, physiological, and biochemical characteristics obtained indicate that the two isolates can be classified into a separate genus, and Ameyamaea chiangmaiensis gen. nov., sp. nov. is proposed. The type strain is isolate AC04(T) (=BCC 15744(T), =NBRC 103196(T)), which has a DNA G+C content of 66.0 mol %. PMID:19809199

Yukphan, Pattaraporn; Malimas, Taweesak; Muramatsu, Yuki; Takahashi, Mai; Kaneyasu, Mika; Potacharoen, Wanchern; Tanasupawat, Somboon; Nakagawa, Yasuyoshi; Hamana, Koei; Tahara, Yasutaka; Suzuki, Ken-ichiro; Tanticharoen, Morakot; Yamada, Yuzo

2009-10-01

272

Mumia flava gen. nov., sp. nov., an actinobacterium of the family Nocardioidaceae.  

PubMed

A novel actinobacterial strain, designated MUSC 201(T), was isolated from a mangrove soil collected from Kuantan, the capital city of Pahang State in Malaysia. The taxonomic status of this strain was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis revealed that strain MUSC 201(T) represented a novel lineage within the class Actinobacteria. Strain MUSC 201(T) formed a distinct clade in the family Nocardioidaceae and was most closely related to the members of the genera Nocardioides (16S rRNA gene sequence similarity, 91.9-95.1?%), Aeromicrobium (92.7-94.6?%), Marmoricola (92.5-93.1?%) and Kribbella (91.5-92.4?%). The cells of this strain were irregular coccoid to short rod shaped. The peptidoglycan contained ll-diaminopimelic acid as diagnostic diamino acid and the peptidoglycan type was A3?. The peptidoglycan cell wall contained ll-diaminopimelic acid, glycine, glutamic acid and alanine in a molar ratio of 1.5?:?0.9?:?1.0?:?1.5. The cell-wall sugars were galactose and rhamnose. The predominant menaquinone was MK-9(H4). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, glycolipid and four unknown phospholipids. The major cellular fatty acids were C18?:?1?9c (30.8?%), C16?:?0 (24.1?%), and 10-methyl C18?:?0 (13.9?%). The DNA G+C content was 72.0±0.1 mol%. On the basis of phylogenetic and phenotypic differences from members of the genera of the family Nocardioidaceae, a novel genus and species, Mumia flava gen. nov., sp. nov. are proposed. The type strain of Mumia flava is MUSC 201(T) (?=?DSM 27763(T)?=?MCCC 1A00646(T)?=?NBRC 109973(T)). PMID:24449791

Lee, Learn-Han; Zainal, Nurullhudda; Azman, Adzzie-Shazleen; Mutalib, Nurul-Syakima Ab; Hong, Kui; Chan, Kok-Gan

2014-05-01

273

Ornithinibacillus gen. nov., with the species Ornithinibacillus bavariensis sp. nov. and Ornithinibacillus californiensis sp. nov.  

PubMed

A Gram-positive, aerobic, rod-shaped, motile, endospore-forming bacterium was isolated from pasteurized milk from Bavaria, Germany. 16S rRNA gene sequence similarities indicated that strain WSBC 24001(T) was most closely related to Virgibacillus species (95.3-96.1 %), Oceanobacillus species (95.6-95.7 %), Bacillus firmus IAM 12464(T) (95.5 %) and Bacillus niacini IFO 15566(T) (95.2 %). However, strain WSBC 24001(T) showed the highest level of sequence similarity to an unnamed strain, MB-9(T) (97.6 %), which was isolated from coastal surface sediments in California. Hence, this strain was included in our study. The genomic DNA G + C contents of strains WSBC 24001(T) and MB-9(T) were 36.4 mol and 40.8 mol%, respectively. The major respiratory quinone of both strains was menaquinone MK-7 and the peptidoglycan type was A4beta (L-orn<--D-Asp). The polar lipid profiles of these strains contained a predominance of diphosphatidylglycerol and moderate to minor amounts of phosphatidylglycerol, an unknown phospholipid and an unknown aminophospholipid. However, strain WSBC 24001(T) could be distinguished from strain MB-9(T) by the presence of an unknown lipid. The fatty acid profiles of the two strains comprised mainly iso- and anteiso-branched acids, but showed some significant quantitative differences in the amounts of certain acids. The DNA-DNA relatedness value (15.5 %) clearly demonstrated that strains WSBC 24001(T) and MB-9(T) are representatives of two different species. On the basis of their phylogenetic position and morphological, physiological and chemotaxonomic properties, a novel genus is proposed, Ornithinibacillus gen. nov., with two novel species, the type species Ornithinibacillus bavariensis sp. nov. (type strain WSBC 24001(T) = DSM 15681(T) = CCM 7096(T)) and Ornithinibacillus californiensis sp. nov. (type strain MB-9(T) = DSM 16628(T) = CCM 7237(T)). PMID:16738118

Mayr, R; Busse, H-J; Worliczek, H L; Ehling-Schulz, M; Scherer, S

2006-06-01

274

Paucisalibacillus globulus gen. nov., sp. nov., a Gram-positive bacterium isolated from potting soil.  

PubMed

A Gram-positive bacterium, designated B22(T), was isolated from potting soil produced in Portugal. This organism is a catalase-positive, oxidase-negative, motile, spore-forming, aerobic rod that grows optimally at 37 degrees C and pH 8.0-8.5. Optimal growth occurs in media containing 1 % (w/v) NaCl, although the organism can grow in 0-8 % NaCl. The cell wall peptidoglycan is of the A4alpha type with a cross-linkage containing d-Asp. The major respiratory quinone is menaquinone 7 and the major fatty acids are anteiso-15 : 0, anteiso-17 : 0 and iso-15 : 0. The DNA G+C content is 37.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain B22(T) formed a new branch within the family Bacillaceae. The novel isolate is phylogenetically closely related to members of genera of moderately halophilic bacilli and formed a coherent cluster with species of the genera Salinibacillus, Virgibacillus, Oceanobacillus and Lentibacillus, supported by bootstrap analysis at a confidence level of 71 %. Strain B22(T) exhibited 16S rRNA gene pairwise sequence similarity values of 94.7-94.3 % with members of the genus Salinibacillus, 95.1-92.8 % with members of the genus Virgibacillus, 94.7-93.2 % with members of the genus Oceanobacillus and 93.1-92.3 % with members of the genus Lentibacillus. On the basis of phylogenetic analysis and physiological and biochemical characteristics, it is proposed that strain B22(T) represents a novel species in a new genus, Paucisalibacillus globulus gen. nov., sp. nov. Strain B22(T) (=LMG 23148(T)=CIP 108857(T)) is the type strain of Paucisalibacillus globulus. PMID:16902018

Nunes, Inês; Tiago, Igor; Pires, Ana Luísa; da Costa, Milton S; Veríssimo, António

2006-08-01

275

Feasibility of a Networked Air Traffic Infrastructure Validation Environment for Advanced NextGen Concepts  

NASA Technical Reports Server (NTRS)

Abstract-Next Generation Air Transportation System (NextGen) applications reliant upon aircraft data links such as Automatic Dependent Surveillance-Broadcast (ADS-B) offer a sweeping modernization of the National Airspace System (NAS), but the aviation stakeholder community has not yet established a positive business case for equipage and message content standards remain in flux. It is necessary to transition promising Air Traffic Management (ATM) Concepts of Operations (ConOps) from simulation environments to full-scale flight tests in order to validate user benefits and solidify message standards. However, flight tests are prohibitively expensive and message standards for Commercial-off-the-Shelf (COTS) systems cannot support many advanced ConOps. It is therefore proposed to simulate future aircraft surveillance and communications equipage and employ an existing commercial data link to exchange data during dedicated flight tests. This capability, referred to as the Networked Air Traffic Infrastructure Validation Environment (NATIVE), would emulate aircraft data links such as ADS-B using in-flight Internet and easily-installed test equipment. By utilizing low-cost equipment that is easy to install and certify for testing, advanced ATM ConOps can be validated, message content standards can be solidified, and new standards can be established through full-scale flight trials without necessary or expensive equipage or extensive flight test preparation. This paper presents results of a feasibility study of the NATIVE concept. To determine requirements, six NATIVE design configurations were developed for two NASA ConOps that rely on ADS-B. The performance characteristics of three existing in-flight Internet services were investigated to determine whether performance is adequate to support the concept. Next, a study of requisite hardware and software was conducted to examine whether and how the NATIVE concept might be realized. Finally, to determine a business case, economic factors were evaluated and a preliminary cost-benefit analysis was performed.

McCormack, Michael J.; Gibson, Alec K.; Dennis, Noah E.; Underwood, Matthew C.; Miller,Lana B.; Ballin, Mark G.

2013-01-01

276

Anaerosalibacter bizertensis gen. nov., sp. nov., a halotolerant bacterium isolated from sludge.  

PubMed

A strictly anaerobic, halotolerant and thermotolerant strain, designated C5BEL(T), was isolated in north Tunisia from storage tanks holding waste generated by the recycling of discarded motor oils. Cells of strain C5BEL(T) were Gram-stain-positive, motile by laterally inserted flagella, straight, and spore-forming. Their two major fatty acids were iso-C(15?:?0) and iso-C(15?:?0) dimethyl acetal. Growth was observed at temperatures of 25-55 °C (optimum, 40 °C) and at pH 6-9 (optimum, pH 7.5). The salinity range for growth was 0-100 g l(-1) NaCl (optimum, 5 g l(-1)). Yeast extract was required for growth. Strain C5BEL(T) was heterotrophic, able to use glucose, pyruvate, succinate, yeast extract, bio-trypticase and peptone, but unable to grow on Casamino acids. Sulfate, thiosulfate, sulfite, elemental sulfur, fumarate, nitrate and nitrite were not reduced. The DNA G+C content of strain C5BEL(T) was 31.1 mol%. 16S rRNA gene sequence analysis indicated that strain C5BEL(T) was a member of the family Clostridiaceae, class Clostridia, phylum Firmicutes and was most closely related to Sporanaerobacter acetigenes Lup33(T) (?=?DSM 13106(T)) (92.4?% similarity). On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain C5BEL(T) can be classified as a novel species in a new genus, for which the name Anaerosalibacter bizertensis gen. nov., sp. nov. is proposed. The type strain of the type species is C5BEL(T) (?=?DSM 23801(T)?=?JCM 17239(T)). PMID:22140152

Rezgui, Raja; Maaroufi, Abderrazak; Fardeau, Marie-Laure; Ben Ali Gam, Zouhaier; Cayol, Jean-Luc; Ben Hamed, Saïd; Labat, Marc

2012-10-01

277

Sulfurisoma sediminicola gen. nov., sp. nov., a facultative autotroph isolated from a freshwater lake.  

PubMed

A novel facultatively autotrophic bacterium, strain BSN1T was isolated from sediment of a freshwater lake in Japan. The cells were rod-shaped, motile and Gram-stain-negative. As sole energy sources for autotrophic growth, the strain oxidized thiosulfate, elemental sulfur and hydrogen. Strain BSN1T was a facultative anaerobe utilizing nitrate as an electron acceptor. Growth was observed at temperatures lower than 34 °C, and the optimum growth was observed at 30-32 °C. The range of pH for growth was pH 6.8-8.8, and the optimum pH was pH 7.8-8.1. The optimum growth of the isolate occurred at concentrations of NaCl less than 50 mM. The G+C content of genomic DNA was 67 mol%. The major component in the fatty acid profile of strain BSN1T grown on fumarate was summed feature 3 (C16:1?7c and/or iso-C15:0 2-OH). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was a member of the class Betaproteobacteria, and it showed the highest sequence similarity with Georgfuchsia toluolica G5G6T (96.2%). Phylogenetic analyses were also performed on genes involved in sulfur oxidation. On the basis of its phylogenetic and phenotypic properties, strain BSN1T (=DSM 26916T=NBRC 109412T) is proposed as the type strain of a novel species of a novel genus, Sulfurisoma sediminicola gen. nov., sp. nov. PMID:24480906

Kojima, Hisaya; Fukui, Manabu

2014-05-01

278

Thermotunica guangxiensis gen. nov., sp. nov., isolated from mushroom residue compost.  

PubMed

A novel thermophilic actinomycete, designated AG2-7T, was isolated from mushroom residue compost in Guangxi University, Nanning, China. The strain grew optimally at 45-60 °C, at pH 7.0 and with 0-3.0% (w/v) NaCl. Vegetative mycelia were branched and whitish to pale yellow without fragmentation. Aerial mycelium was abundant, whitish and differentiated into long chains of spores, with a membranous structure or tunica partially covering the surface of aerial hyphae. The non-motile spores were oval in shape with a ridged surface. Strain AG-27T contained meso-diaminopimelic acid as the diagnostic diamino acid, and the whole-cell sugars were galactose and ribose. Major fatty acids were iso-C16:0 (27.51%), iso-C17:0 (10.47%) and anteiso-C17:0 (12.01%). MK-9(H4) was the predominant menaquinone. The polar phospholipids were diphosphatidylglycerol, ninhydrin-positive glycophospholipid, phosphatidylinositol, phosphatidylinositol mannoside, phosphatidylethanolamine, phosphatidylmethylethanolamine, an unknown phospholipid and unknown glucosamine-containing phospholipids. The G+C content of the genomic DNA was 63.6 mol%. 16S rRNA gene sequence analysis showed that the organism belonged to the family Pseudonocardiaceae, suborder Pseudonocardineae and showed more than 5% divergence from other members of the family. Based on the phenotypic and phylogenetic data, strain AG2-7T represents a novel species of a new genus in the family Pseudonocardiaceae, for which the name Thermotunica guangxiensis gen. nov., sp. nov. is proposed. The type strain of the type species is AG2-7T (=ATCC BAA-2499T=CGMCC 4.7099T). PMID:24488931

Wu, Hao; Lian, Yunpeng; Liu, Bin; Ren, Yanling; Qin, Peisheng; Huang, Fuchang

2014-05-01

279

Psychroglaciecola arctica gen. nov., sp. nov., isolated from Arctic glacial foreland soil.  

PubMed

A novel pink-pigmented, facultatively methylotrophic strain, designated M6-76T, was isolated from glacial foreland soil near Ny-Ålesund, Svalbard Archipelago, Norway. Cells of strain M6-76T were rod-shaped (0.4-0.7×0.8-2.0 µm), Gram-stain-negative, aerobic and motile by a single polar flagellum. Growth occurred at 4-28 °C (optimum 18 °C) and at pH 5-8 (optimum pH 7). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M6-76T belonged to the family Methylobacteriaceae. The 16S rRNA gene sequence of the novel strain showed 94.6%, 94.0% and 93.9% sequence similarity to those of Methylobacterium salsuginis MRT, Methylobacterium organophilum ATCC 27886T and Microvirga subterranea FaiI4T, respectively. Cells could utilize methanol as the sole source of carbon and energy but not formate. The major respiratory quinone was Q-10. The polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and two unknown polar lipids. The predominant cellular fatty acids were summed feature 8 (C18:1?7c and/or C18:1?6c), summed feature 3 (C16:1?6c and/or C16:1?7c) and C16:0. The DNA G+C content was 67 mol%. The polyphasic data presented in this study indicated that the isolate should be classified as representing a novel species of a new genus within the family Methylobacteriaceae. The name Psychroglaciecola arctica gen. nov., sp. nov. is therefore proposed for the isolate. The type strain of the type species is M6-76T (=CCTCC AB 2013033T=KACC 17684T). PMID:24556636

Qu, Zhihao; Jiang, Fan; Chang, Xulu; Qiu, Xia; Ren, Lvzhi; Fang, Chengxiang; Peng, Fang

2014-05-01

280

Pseudogracilibacillus auburnensis gen. nov., sp. nov., isolated from the rhizosphere of Zea mays.  

PubMed

A Gram-positive-staining, aerobic, endospore-forming bacterium, strain P-207(T), was isolated from a rhizosphere soil sample in Auburn, AL, USA. On the basis of 16S rRNA gene sequence comparisons, strain P-207(T) was grouped in the vicinity of representatives of the genera Virgibacillus, Ornithinibacillus, Cerasibacillus, Lentibacillus and Oceanobacillus, but could not be assigned clearly to any of these genera. The highest similarity was found to the sequence of Virgibacillus carmonensis LMG 20964(T) (94.4?%); however, the 16S rRNA gene sequence similarity to the type strain of the type species of Virgibacillus, Virgibacillus pantothenticus, was only 92.9?%. The quinone system of strain P-207(T) consisted predominantly of menaquinone MK-7. The polar lipid profile exhibited the major lipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and moderate to minor amounts of several unidentified phospholipids, glycolipids and phosphoglycolipids, an aminophospholipid and an aminolipid. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid and the polyamine pattern contained predominantly spermidine and spermine. The major fatty acids were anteiso-C15?:?0, anteiso-C17?:?0, iso-C16?:?0 and iso-C15?:?0. The G+C content of the genomic DNA was 34 mol%. Because of the low sequence similarity of strain P-207(T) to all representatives of Virgibacillus, Ornithinibacillus, Cerasibacillus, Lentibacillus and Oceanobacillus, which was always <95?%, and its unique lipid pattern, we propose that strain P-207(T) represents a novel species in a new genus, for which the name Pseudogracilibacillus auburnensis gen. nov., sp. nov. is proposed. The type strain of Pseudogracilibacillus auburnensis is P-207(T) (?=?CCM 8509(T)?=?LMG 28212(T)?=?CIP 110797(T)). PMID:24801155

Glaeser, Stefanie P; McInroy, John A; Busse, Hans-Jürgen; Kämpfer, Peter

2014-07-01

281

Siphonobacter aquaeclarae gen. nov., sp. nov., a novel member of the family 'Flexibacteraceae', phylum Bacteroidetes.  

PubMed

A Gram-negative bacterium, designated P2(T), was isolated from the biofilm developed on the inner surface of an ultrapure cooling water system in a Hungarian power plant and was characterized by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain P2(T) was affiliated with the family 'Flexibacteraceae' in the phylum Bacteroidetes. Its closest relative was Flectobacillus lacus CL-GP79(T) (88.7?% 16S rRNA gene sequence similarity) followed by Arcicella rosea TW5(T) (86.5?%), Arcicella aquatica NO-502(T) (86.4?%), Flectobacillus roseus GFA-11(T) (86.3?%) and Flectobacillus major DSM 103(T) (85.4?%). Cells of strain P2(T) were facultatively anaerobic, non-motile rods. The major fatty acids were C(16?:?1)?5c (42.5?%), iso-C(15?:?0) 2-OH (17.2?%), iso-C(17?:?0) 3-OH (16.1?%) and iso-C(15?:?0) (8.5?%). The major menaquinone was MK-7 and the predominant polar lipid was phosphatidylethanolamine. The DNA G+C content was 54.5 mol%. Thus, the phenotypic and genotypic analyses clearly showed that strain P2(T) is considerably different from members of other genera in the family 'Flexibacteraceae'. Based on these results, it is concluded that strain P2(T) represents a novel species in a new genus, for which the name Siphonobacter aquaeclarae gen. nov., sp. nov. is proposed, with type strain P2(T) (=DSM 21668(T) =NCAIM B 02328(T)). PMID:20008110

Táncsics, András; Kéki, Zsuzsa; Márialigeti, Károly; Schumann, Peter; Tóth, Erika M

2010-11-01

282

Cascadiacarpa spinosa gen. et sp. nov. (Fagaceae): castaneoid fruits from the Eocene of Vancouver Island, Canada.  

PubMed

Documenting the paleodiversity of well-studied angiosperm families serves to broaden their circumscription while also providing a time-specific reference point to mark the first occurrence of characters and appearance of lineages. More than 80 anatomically preserved specimens of spiny, cupulate fruits in various developmental stages have been studied from the Eocene Appian Way locality of Vancouver Island, British Columbia, Canada. Details of internal anatomy and external morphology are known for the cupules, fruits, and pedicels. Cupule spines branch and are often borne in clusters. Cupules lack clear sutures and are adnate to a single nut that is enclosed entirely with the exception of the apical stylar protrusion of the pistil. A central hollow cylinder of vascular tissue can be seen extending up the peduncle to the base of the fruit and along the inner wall of the cupule. The fruit has a sclerotic outer pericarp that grades into a parenchymatous mesocarp and a sclerotic endocarp lining the locules. Early in development, the two locules are divided by a thin septum to which the ovules are attached. Only one seed develops to maturity as evidenced by an embryo occupying the locule alongside an abortive apical ovule. Three-dimensional reconstructions of these fruits have allowed for comparisons to both extinct and extant fagaceous taxa. The Appian Way fruits are most similar to extant Castanopsis species (Fagaceae) but differ in having only two locules. Cascadiacarpa spinosa gen. et sp. nov. Mindell, Stockey et Beard is the first occurence of a bipartite gynoecium and earliest known occurrence of hypogeous fruits in Fagaceae. The appearance of Casacadiacarpa in the Eocene of British Columbia supports a Paleogene radiation of the family. The numerous derived characters of these fruits show that evalvate, spiny, single-fruited cupules of Fagaceae were present in the Paleogene of North America. PMID:21636406

Mindell, Randal A; Stockey, Ruth A; Beard, Graham

2007-03-01

283

Genea, Genabea and Gilkeya gen. nov.: ascomata and ectomycorrhiza formation in a Quercus woodland.  

PubMed

Genea and Genabea are considered ectomycorrhizal (EM) symbionts of higher plants, but because of their hypogeous habit, dark coloration and the small size of their ascomata, relatively little is known about these genera. Ascomata of six morphological species of Genea and one of Genabea were frequently collected at a single site in xeric Quercus woodlands of California's Sierra Nevada foothills. While most collections were easily referred to known species, those putatively identified as Genea harknessii and Genea arenaria were problematic. Genea harknessii collections appeared relatively homogenous based on morphology, but significant ITS variation revealed by rDNA sequencing suggested cryptic species diversity. Specimens of G. arenaria approximated the brief, original species description except for abundant clumps of septate setae formed at the apex of peridial warts. To verify the identity of this species we reexamined the holotype and analyzed morphology and ITS sequences of G. arenaria ascomata from a wide geographic range. To authenticate the EM status of Genea and Genabea with Quercus we collected healthy EM of Quercus douglasii and Quercus wislizenii and compared their ITS sequences to those from ascomata. We detected nine distinct ITS types of Genea and Genabea on roots. Two new species described here as Genea bihymeniata sp. nov. and Genea cazaresii sp. nov., were discovered during study of herbarium specimens. A phylogenetic analysis of 28 s rDNA from Genea and Genabea indicated three distinct lineages: Genea, Genabea and a third represented by Genea intermedia. For the latter we propose Gilkeya gen. nov. to accommodate the single known species, Gilkeya compacta comb. nov. A dichotomous key to all known Genea, Genabea and Gilkeya spp. from western North America is presented. PMID:17256574

Smith, Matthew E; Trappe, James M; Rizzo, David M

2006-01-01

284

Stomatobaculum longum gen. nov., sp. nov., an obligately anaerobic bacterium from the human oral cavity.  

PubMed

A strictly anaerobic Gram-stain-variable but positive by structure, non-spore-forming bacterium designated Lachnospiraceae bacterium ACC2 strain DSM 24645(T) was isolated from human subgingival dental plaque. Bacterial cells were 4-40 µm long non-motile rods, often swollen and forming curved filaments up to 200 µm. Cells contained intracellular, poorly crystalline, nanometre-sized iron- and sulfur-rich particles. The micro-organism was able to grow on yeast extract, trypticase peptone, milk, some sugars and organic acids. The major metabolic end-products of glucose fermentation were butyrate, lactate, isovalerate and acetate. The growth temperature and pH ranges were 30-42 °C and 4.9-7.5, respectively. Major fatty acids were C14?:?0, C14?:?0 DMA (dimethyl aldehyde), C16?:?0, C16?:?1?7c DMA. The whole-cell hydrolysate contained meso-diaminopimelic acid, indicating peptidoglycan type A1?. The DNA G+C content was calculated to be 55.05 mol% from the whole-genome sequence and 55.3 mol% as determined by HPLC. There were no predicted genes responsible for biosynthesis of respiratory lipoquinones, mycolic acids and lipopolysaccharides. Genes associated with synthesis of teichoic and lipoteichoic acids, diaminopimelic acid, polar lipids and polyamines were present. According to the 16S rRNA gene sequence phylogeny, strain DSM 24645(T) formed, together with several uncultured oral clones, a separate branch within the family Lachnospiraceae, with the highest sequence similarity to the type strain of Moryella indoligenes at 94.2?%. Based on distinct phenotypic and genotypic characteristics, we suggest that strain DSM 24645(T) represents a novel species in a new genus, for which the name Stomatobaculum longum gen. nov., sp. nov. is proposed. The type strain of Stomatobaculum longum is DSM 24645(T) (?=?HM-480(T); deposited in BEI Resources, an NIH collection managed by the ATCC). PMID:22843721

Sizova, Maria V; Muller, Paul; Panikov, Nicolai; Mandalakis, Manolis; Hohmann, Tine; Hazen, Amanda; Fowle, William; Prozorov, Tanya; Bazylinski, Dennis A; Epstein, Slava S

2013-04-01

285

Control Control Control: A Reassessment and Comparison of GenBank and Chromatogram mtDNA Sequence Variation in Baltic Grey Seals (Halichoerus grypus)  

PubMed Central

Genetic data can provide a powerful tool for those interested in the biology, management and conservation of wildlife, but also lead to erroneous conclusions if appropriate controls are not taken at all steps of the analytical process. This particularly applies to data deposited in public repositories such as GenBank, whose utility relies heavily on the assumption of high data quality. Here we report on an in-depth reassessment and comparison of GenBank and chromatogram mtDNA sequence data generated in a previous study of Baltic grey seals. By re-editing the original chromatogram data we found that approximately 40% of the grey seal mtDNA haplotype sequences posted in GenBank contained errors. The re-analysis of the edited chromatogram data yielded overall similar results and conclusions as the original study. However, a significantly different outcome was observed when using the uncorrected dataset based on the GenBank haplotypes. We therefore suggest disregarding the existing GenBank data and instead using the correct haplotypes reported here. Our study serves as an illustrative example reiterating the importance of quality control through every step of a research project, from data generation to interpretation and submission to an online repository. Errors conducted in any step may lead to biased results and conclusions, and could impact management decisions.

Fietz, Katharina; Graves, Jeff A.; Olsen, Morten Tange

2013-01-01

286

WallGen, software to construct layered cellulose-hemicellulose networks and predict their small deformation mechanics.  

PubMed

We understand few details about how the arrangement and interactions of cell wall polymers produce the mechanical properties of primary cell walls. Consequently, we cannot quantitatively assess if proposed wall structures are mechanically reasonable or assess the effectiveness of proposed mechanisms to change mechanical properties. As a step to remedying this, we developed WallGen, a Fortran program (available on request) building virtual cellulose-hemicellulose networks by stochastic self-assembly whose mechanical properties can be predicted by finite element analysis. The thousands of mechanical elements in the virtual wall are intended to have one-to-one spatial and mechanical correspondence with their real wall counterparts of cellulose microfibrils and hemicellulose chains. User-defined inputs set the properties of the two polymer types (elastic moduli, dimensions of microfibrils and hemicellulose chains, hemicellulose molecular weight) and their population properties (microfibril alignment and volume fraction, polymer weight percentages in the network). This allows exploration of the mechanical consequences of variations in nanostructure that might occur in vivo and provides estimates of how uncertainties regarding certain inputs will affect WallGen's mechanical predictions. We summarize WallGen's operation and the choice of values for user-defined inputs and show that predicted values for the elastic moduli of multinet walls subject to small displacements overlap measured values. "Design of experiment" methods provide systematic exploration of how changed input values affect mechanical properties and suggest that changing microfibril orientation and/or the number of hemicellulose cross-bridges could change wall mechanical anisotropy. PMID:20007450

Kha, Hung; Tuble, Sigrid C; Kalyanasundaram, Shankar; Williamson, Richard E

2010-02-01

287

GenSeq: An updated nomenclature and ranking for genetic sequences from type and non-type sources.  

PubMed

An improved and expanded nomenclature for genetic sequences is introduced that corresponds with a ranking of the reliability of the taxonomic identification of the source specimens. This nomenclature is an advancement of the "Genetypes" naming system, which some have been reluctant to adopt because of the use of the "type" suffix in the terminology. In the new nomenclature, genetic sequences are labeled "genseq," followed by a reliability ranking (e.g., 1 if the sequence is from a primary type), followed by the name of the genes from which the sequences were derived (e.g., genseq-1 16S, COI). The numbered suffix provides an indication of the likely reliability of taxonomic identification of the voucher. Included in this ranking system, in descending order of taxonomic reliability, are the following: sequences from primary types - "genseq-1," secondary types - "genseq-2," collection-vouchered topotypes - "genseq-3," collection-vouchered non-types - "genseq-4," and non-types that lack specimen vouchers but have photo vouchers - "genseq-5." To demonstrate use of the new nomenclature, we review recently published new-species descriptions in the ichthyological literature that include DNA data and apply the GenSeq nomenclature to sequences referenced in those publications. We encourage authors to adopt the GenSeq nomenclature (note capital "G" and "S" when referring to the nomenclatural program) to provide a searchable tag (e.g., "genseq"; note lowercase "g" and "s" when referring to sequences) for genetic sequences from types and other vouchered specimens. Use of the new nomenclature and ranking system will improve integration of molecular phylogenetics and biological taxonomy and enhance the ability of researchers to assess the reliability of sequence data. We further encourage authors to update sequence information on databases such as GenBank whenever nomenclatural changes are made. PMID:24223486

Chakrabarty, Prosanta; Warren, Melanie; Page, Lawrence M; Baldwin, Carole C

2013-01-01

288

GIDL: a rule based expert system for GenBank Intelligent Data Loading into the Molecular Biodiversity database  

PubMed Central

Background In the scientific biodiversity community, it is increasingly perceived the need to build a bridge between molecular and traditional biodiversity studies. We believe that the information technology could have a preeminent role in integrating the information generated by these studies with the large amount of molecular data we can find in bioinformatics public databases. This work is primarily aimed at building a bioinformatic infrastructure for the integration of public and private biodiversity data through the development of GIDL, an Intelligent Data Loader coupled with the Molecular Biodiversity Database. The system presented here organizes in an ontological way and locally stores the sequence and annotation data contained in the GenBank primary database. Methods The GIDL architecture consists of a relational database and of an intelligent data loader software. The relational database schema is designed to manage biodiversity information (Molecular Biodiversity Database) and it is organized in four areas: MolecularData, Experiment, Collection and Taxonomy. The MolecularData area is inspired to an established standard in Generic Model Organism Databases, the Chado relational schema. The peculiarity of Chado, and also its strength, is the adoption of an ontological schema which makes use of the Sequence Ontology. The Intelligent Data Loader (IDL) component of GIDL is an Extract, Transform and Load software able to parse data, to discover hidden information in the GenBank entries and to populate the Molecular Biodiversity Database. The IDL is composed by three main modules: the Parser, able to parse GenBank flat files; the Reasoner, which automatically builds CLIPS facts mapping the biological knowledge expressed by the Sequence Ontology; the DBFiller, which translates the CLIPS facts into ordered SQL statements used to populate the database. In GIDL Semantic Web technologies have been adopted due to their advantages in data representation, integration and processing. Results and conclusions Entries coming from Virus (814,122), Plant (1,365,360) and Invertebrate (959,065) divisions of GenBank rel.180 have been loaded in the Molecular Biodiversity Database by GIDL. Our system, combining the Sequence Ontology and the Chado schema, allows a more powerful query expressiveness compared with the most commonly used sequence retrieval systems like Entrez or SRS.

2012-01-01

289

Proposal of Umezawaea gen. nov., a new genus of the Actinosynnemataceae related to Saccharothrix, and transfer of Saccharothrix tangerinus Kinoshita et al. 2000 as Umezawaea tangerina gen. nov., comb. nov.  

PubMed

In the course of phylogenetic analyses of the taxa within the suborder Pseudonocardineae, it was observed that Saccharothrix tangerinus MK27-91F2(T) was misplaced in the genus Saccharothrix. After a detailed examination of nucleotide signatures in the 16S rRNA gene sequence along with the morphological and chemotaxonomic characteristics of this strain, which are different from those of all species of Saccharothrix as well as the other genera within the suborder, it was concluded that this strain represents a new genus, for which the name Umezawaea gen. nov. is proposed. Pseudosporangia are produced on the aerial mycelium, the whole-cell sugar pattern consists of galactose, mannose and ribose, phosphatidylethanolamine, phosphatidylinositol and lyso-phosphatidylethanolamine are the predominant phospholipids and MK-9(H(4)) is the predominant menaquinone. The type species of the proposed new genus is Umezawaea tangerina gen. nov., comb. nov., with the type strain MK27-91F2(T) (=NRRL B-24463(T) =DSM 44720(T) =FERM P-16053(T) =JCM 10302(T) =NBRC 16184(T)). PMID:18048721

Labeda, D P; Kroppenstedt, R M

2007-12-01

290

Modeling and Evaluating Pilot Performance in NextGen: Review of and Recommendations Regarding Pilot Modeling Efforts, Architectures, and Validation Studies  

NASA Technical Reports Server (NTRS)

NextGen operations are associated with a variety of changes to the national airspace system (NAS) including changes to the allocation of roles and responsibilities among operators and automation, the use of new technologies and automation, additional information presented on the flight deck, and the entire concept of operations (ConOps). In the transition to NextGen airspace, aviation and air operations designers need to consider the implications of design or system changes on human performance and the potential for error. To ensure continued safety of the NAS, it will be necessary for researchers to evaluate design concepts and potential NextGen scenarios well before implementation. One approach for such evaluations is through human performance modeling. Human performance models (HPMs) provide effective tools for predicting and evaluating operator performance in systems. HPMs offer significant advantages over empirical, human-in-the-loop testing in that (1) they allow detailed analyses of systems that have not yet been built, (2) they offer great flexibility for extensive data collection, (3) they do not require experimental participants, and thus can offer cost and time savings. HPMs differ in their ability to predict performance and safety with NextGen procedures, equipment and ConOps. Models also vary in terms of how they approach human performance (e.g., some focus on cognitive processing, others focus on discrete tasks performed by a human, while others consider perceptual processes), and in terms of their associated validation efforts. The objectives of this research effort were to support the Federal Aviation Administration (FAA) in identifying HPMs that are appropriate for predicting pilot performance in NextGen operations, to provide guidance on how to evaluate the quality of different models, and to identify gaps in pilot performance modeling research, that could guide future research opportunities. This research effort is intended to help the FAA evaluate pilot modeling efforts and select the appropriate tools for future modeling efforts to predict pilot performance in NextGen operations.

Wickens, Christopher; Sebok, Angelia; Keller, John; Peters, Steve; Small, Ronald; Hutchins, Shaun; Algarin, Liana; Gore, Brian Francis; Hooey, Becky Lee; Foyle, David C.

2013-01-01

291

search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information  

PubMed Central

Background Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. Results We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user’s query, advanced data searching based on the specified user’s query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. Conclusions search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/.

2013-01-01

292

Tatumella ptyseos gen. nov., sp. nov., a member of the family Enterobacteriaceae found in clinical specimens.  

PubMed Central

The name Tatumella ptyseos gen. nov., sp. nov., is proposed for a group of organisms (previously called group EF-9) isolated from clinical sources in the United States, Canada, and Puerto Rico. A total of 68% of these isolates were from sputum specimens. T. ptyseos strains are gram-negative, oxidase-negative, fermentative rods that grow on MacConkey agar. The distinctive biochemical characteristics of 44 T. ptyseos isolates were as follows: acid but no gas from D-glucose, sucrose, and, usually (71%), D-xylose (62% delayed); no acid from lactose, maltose, or D-mannitol; negative tests for indole, urea, methyl red, gelatin, L-lysine decarboxylase, and L-ornithine decarboxylase; L-arginine dihydrolase variable; phenylalanine deaminase positive; Voges-Proskauer positive by the Coblentz method but negative by the O'Meara method; nonmotile at 36 degrees C but 66% weakly motile (30% delayed) at 25 degrees C; Simmons citrate positive at 25 degrees C (89%) but Simmons citrate negative at 36 degrees C. Deoxyribonucleic acid-deoxyribonucleic acid relatedness studies on 26 T. ptyseos strains showed that they were 80 to 100% related at 60 degrees C, which indicated that they comprise a single species. The deoxyribonucleic acid relatedness to other species within the Enterobacteriaceae was 7 to 38%. This is evidence that this species belongs in this family, is distinct from all described species and is best placed in a new genus. The T. ptyseos isolates studied were susceptible to all of the antimicrobial agents tested by broth dilution; these antimicrobial agents were amikacin, ampicillin, cephalothin, chloramphenicol, gentamicin, kanamycin, tetracycline, and tobramycin. Three striking differences between T. ptyseos and other members of the Enterobacteriaceae were its large zone of inhibition around penicillin (mean diameter 24 mm), its tendency to die on some laboratory media (such as blood agar) within 7 days, and its small number (usually one) of flagella. Strain H36 (=ATCC 33301, =CDC D6168, =CDC 9591-78) is the type strain of this new species. T. ptyseos is the type species for the genus Tatumella. Images

Hollis, D G; Hickman, F W; Fanning, G R; Farmer, J J; Weaver, R E; Brenner, D J

1981-01-01

293

Kosmotoga olearia gen. nov., sp. nov., a thermophilic, anaerobic heterotroph isolated from an oil production fluid.  

PubMed

A novel thermophilic, heterotrophic bacterium, strain TBF 19.5.1(T), was isolated from oil production fluid at the Troll B oil platform in the North Sea. Cells of strain TBF 19.5.1(T) were non-motile rods with a sheath-like structure, or toga. The strain was Gram-negative and grew at 20-80 degrees C (optimum 65 degrees C), pH 5.5-8.0 (optimum pH 6.8) and NaCl concentrations of 10-60 g l(-1) (optimum 25-30 g l(-1)). For a member of the order Thermotogales, the novel isolate is capable of unprecedented growth at low temperatures, with an optimal doubling time of 175 min (specific growth rate 0.24 h(-1)) and a final optical density of >1.4 when grown on pyruvate at 37 degrees C. Various carbohydrates, proteinaceous compounds and pyruvate served as growth substrates. Thiosulfate, but not elemental sulfur, enhanced growth of the isolate. Sulfate also enhanced growth, but sulfide was not produced. The strain grew in the presence of up to approximately 15 % oxygen, but only if cysteine was included in the medium. Growth of the isolate was inhibited by acetate, lactate and propionate, while butanol and malate prevented growth. The major fermentation products formed on maltose were hydrogen, carbon dioxide and acetic acid, with traces of ethanol and propionic acid. The G+C content of the genomic DNA was 42.5 mol%. Phylogenetic analyses of the 16S and 23S rRNA gene sequences as well as 29 protein-coding ORFs placed the strain within the bacterial order Thermotogales. Based on the phylogenetic analyses and the possession of a variety of physiological characteristics not previously found in any species of this order, it is proposed that the strain represents a novel species of a new genus within the family Thermotogaceae, order Thermotogales. The name Kosmotoga olearia gen. nov., sp. nov. is proposed. The type strain of Kosmotoga olearia is TBF 19.5.1(T) (=DSM 21960(T) =ATCC BAA-1733(T)). PMID:19643902

Dipippo, Jonathan L; Nesbø, Camilla L; Dahle, Håkon; Doolittle, W Ford; Birkland, Nils-Kåre; Noll, Kenneth M

2009-12-01

294

Polycladomyces abyssicola gen. nov., sp. nov., a thermophilic filamentous bacterium isolated from hemipelagic sediment.  

PubMed

A novel filamentous bacterium, designated strain JIR-001(T), was isolated from hemipelagic sediment in deep seawater. This strain was non-motile, Gram-positive, aerobic, heterotrophic and thermophilic; colonies were of infinite form and ivory coloured with wrinkles between the centre and the edge of the colony on ISP2 medium. The isolate grew aerobically at 55-73 °C with the formation of aerial mycelia; spores were produced singly along the aerial mycelium. These morphological features show some similarities to those of the type strains of some species belonging to the family Thermoactinomycetaceae. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain JIR-001(T) belongs to the family Thermoactinomycetaceae within the class Bacilli. Similarity levels between the 16S rRNA gene sequence of strain JIR-001(T) and those of the type strains of Thermoactinomycetaceae species were 85.5-93.5%; highest sequence similarity was with Melghirimyces algeriensis NariEX(T). In the DNA-DNA hybridization assays between strain JIR-001(T) and its phylogenetic neighbours the mean hybridization levels with Melghirimyces algeriensis NariEX(T), Planifilum fimeticola H0165(T), Planifilum fulgidum 500275(T) and Planifilum yunnanense LA5(T) were 5.3-7.5, 2.3-4.7, 2.1-4.8 and 2.5-4.9%, respectively. The DNA G+C content of strain JIR-001(T) was 55.1 mol%. The major fatty acids were iso-C15:0, iso-C17:0, iso-C16:0 and C16:0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, glucolipid, phosphatidylserine, an amino-group containing phospholipid, an unknown phospholipid and two unknown lipids. The predominant menaquinone was MK-7 and the cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine. On the basis of phenotypic characteristics and 16S rRNA gene sequence comparisons, strain JIR-001(T) is considered to represent a novel species in a new genus of the family Thermoactinomycetaceae, for which the name Polycladomyces abyssicola gen. nov., sp. nov. is proposed. The type strain of Polycladomyces abyssicola is JIR-001(T) (=JCM 18147(T)=CECT 8074(T)). PMID:23024147

Tsubouchi, Taishi; Shimane, Yasuhiro; Mori, Kozue; Usui, Keiko; Hiraki, Toshiki; Tame, Akihiro; Uematsu, Katsuyuki; Maruyama, Tadashi; Hatada, Yuji

2013-06-01

295

The Australian Monstrilloida (Crustacea: Copepoda) I. Monstrillopsis Sars, Maemonstrilla Grygier & Ohtsuka, and Australomonstrillopsis gen. nov.  

PubMed

Monstrilloid copepods were collected during zooplankton surveys in reef and coastal areas of Australia. Representatives of all four genera of the Monstrilloida (Monstrilla Dana, Monstrillopsis Sars, Cymbasoma Thompson, and Maemonstrilla Grygier & Ohtsuka) were recorded. In this contribution a taxonomic analysis of specimens belonging to the latter two genera is provided, and a new genus described. The genus Monstrillopsis was represented exclusively by male specimens, on the basis of which three new species are described: Mon. hastata sp. nov., Mon. boonwurrungorum sp. nov., and Mon. nanus sp. nov. These are distinguished from each other and previously described species of this genus by details of the genital complex (or genital apparatus), body size, ornamentation of the cephalic surface, number of caudal setae, and characteristic modifications of the fifth antennular segment. All have distinctive characters not associated with sexual modifications, which will ease the task of matching females collected in future studies. Australomonstrillopsis gen. nov. is proposed to accommodate a male specimen with a unique combination of characters including massively developed caudal rami, cephalic perioral protuberances, and absence of an inner seta on the first exopodal segment of legs 1-4, among other characters. The new genus is monotypic and contains A. crassicaudata sp. nov. Three of the four new species of Maemonstrilla (Mae. ohtsukai sp. nov., Mae. hoi sp. nov., and Mae. protuberans sp. nov.) belong to the Mae. hyottoko species group, and the remaining one, Mae. crenulata sp. nov., belongs to the Mae. turgida group. Each of the new species of Maemonstrilla from Australia can be distinguished from its known congeners by a unique combination of characters including the type of body reticulation, body size, antennule and body proportions, distinctive characters of the swimming legs, details of the antennular armature, and the presence/absence of a posteroventral process on the genital compound somite. With the addition of the four new species of Monstrillopsis and the four of Maemonstrilla described herein, the number of species in these genera has increased to 13 and 11 species, respectively. In no case did congeneric species co-occur, hinting that there may be a rich species diversity yet to be discovered within the Australian Monstrilloida. PMID:24871727

Suárez-Morales, Eduardo; Mckinnon, A David

2014-01-01

296

Polymorphobacter multimanifer gen. nov., sp. nov., a polymorphic bacterium isolated from antarctic white rock.  

PubMed

A Gram-stain-negative, non-spore-forming, aerobic, oligotrophic bacterium (strain 262-7(T)) was isolated from a crack of white rock collected in the Skallen region of Antarctica. Strain 262-7(T) grew at temperatures between -4 and 30 °C, with optimal growth at 25 °C. The pH range for growth was between pH 6.0 and 9.0, with optimal growth at approximately pH 7.0. The NaCl concentration range allowing growth was between 0.0 and 1.0?%, with an optimum of 0.5?%. Strain 262-7(T) showed an unprecedented range of morphological diversity in response to growth conditions. Cells grown in liquid medium were circular or ovoid with smooth surfaces in the lag phase. In the exponential phase, ovoid cells with short projections were observed. Cells in the stationary phase possessed long tentacle-like projections intertwined intricately. By contrast, cells grown on agar plate medium or in liquid media containing organic compounds at low concentration exhibited short- and long-rod-shaped morphology. These projections and morphological variations clearly differ from those of previously described bacteria. Ubiquinone 10 was the major respiratory quinone. The major fatty acids were C17?:?1?6c (28.2?%), C16?:?1?7c (22.6?%), C18?:?1?7c (12.9?%) and C15?:?0 2-OH (12.3?%). The G+C content of genomic DNA was 68.0 mol%. Carotenoids were detected from the cells. Comparative analyses of 16S rRNA gene sequences indicated that strain 262-7(T) belongs to the family Sphingomonadaceae, and that 262-7(T) should be distinguished from known genera in the family Sphingomonadaceae. According to the phylogenetic position, physiological characteristics and unique morphology variations, strain 262-7(T) should be classified as a representative of a novel genus of the family Sphingomonadaceae. Here, a novel genus and species with the name Polymorphobacter multimanifer gen. nov., sp. nov. is proposed (type strain 262-7(T)?=?JCM 18140(T)?=?ATCC BAA-2413(T)). The novel species was named after its morphological diversity and formation of unique projections. PMID:24651306

Fukuda, Wakao; Chino, Yohzo; Araki, Shigeo; Kondo, Yuka; Imanaka, Hiroyuki; Kanai, Tamotsu; Atomi, Haruyuki; Imanaka, Tadayuki

2014-06-01

297

Methyloparacoccus murrellii gen. nov., sp. nov., a methanotroph isolated from pond water.  

PubMed

Two novel methanotrophic strains, R-49797(T) and OS501, were isolated from pond water in South Africa and Japan, respectively. Strains R-49797(T) and OS501 shared 99.7?% 16S rRNA gene sequence similarity. Cells were Gram-stain-negative, non-motile cocci with a diplococcoid tendency and contained type I methanotroph intracytoplasmic membranes. The pmoA gene encoding particulate methane monooxygenase was present. Soluble methane monoooxygenase (sMMO) activity, the mmoX gene encoding sMMO and the nifH gene encoding nitrogenase were not detected. Methane and methanol were utilized as sole carbon source. The strains grew optimally at 25-33 °C (range 20-37 °C) and at pH 6.3-6.8 (range 5.8-9.0). The strains did not support growth in media supplemented with 1?% (w/v) NaCl. For both strains, the two major fatty acids were C16?:?1?7c and C16?:?0 and the DNA G+C content was 65.6 mol%. The isolates belong to the family Methylococcaceae of the class Gammaproteobacteria and cluster most closely among the genera Methylocaldum, Methylococcus and Methylogaea, with a 16S rRNA gene sequence similarity of 94.2?% between strain R-49797(T) and its closest related type strain (Methylocaldum gracile VKM 14L(T)). Based on the low 16S rRNA gene sequence similarities with its nearest phylogenetic neighbouring genera, the formation of a separate lineage based on 16S rRNA and pmoA gene phylogenetic analysis, and the unique combination of phenotypic characteristics of the two isolated strains compared with the genera Methylocaldum, Methylococcus and Methylogaea, we propose to classify these strains as representing a novel species of a new genus, Methyloparacoccus murrellii gen. nov., sp. nov., within the family Methylococcaceae. The type strain of Methyloparacoccus murrellii is R-49797(T) (?=?LMG 27482(T)?=?JCM 19379(T)). PMID:24676728

Hoefman, Sven; van der Ha, David; Iguchi, Hiroyuki; Yurimoto, Hiroya; Sakai, Yasuyoshi; Boon, Nico; Vandamme, Peter; Heylen, Kim; De Vos, Paul

2014-06-01

298

Chalicogloea cavernicola gen. nov., sp. nov. (Chroococcales, Cyanobacteria), from low-light aerophytic environments: combined molecular, phenotypic and ecological criteria.  

PubMed

This work characterizes a unicellular cyanobacterium with nearly spherical cells and thin-outlined sheaths that divide irregularly, forming small packets immersed in a diffluent mucilaginous layer. It was isolated growing on calcite speleothems and walls in a show cave in Collbató (Barcelona, Spain). Spectral confocal laser and transmission electron microscopy were used to describe the morphology, fine structure and thylakoid arrangement. The pigments identified were phycoerythrin, phycocyanin, allophycocyanin and chlorophyll a. Three-dimensional reconstructions, generated from natural fluorescence z-stacks, revealed a large surface area of nearly flat, arm-like thylakoidal membranes connected to each other and forming a unified structure in a way that, to our knowledge, has never been described before. Phylogenetic analyses using the 16S rRNA gene sequence showed 95% similarity to strain Chroococcus sp. JJCM (GenBank accession no. AM710384). The diacritical phenotypic features do not correspond to any species currently described, and the genetic traits support the strain being classified as the first member of an independent genus in the order Chroococcales and the family Chroococcaceae. Hence, we propose the name Chalicogloea cavernicola gen. nov., sp. nov. under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants. The type strain of Chalicogloea cavernicola is COLL 3(T) (=CCALA 975(T) =CCAP 1424/1(T)). PMID:23178723

Roldán, M; Ramírez, M; del Campo, J; Hernández-Mariné, M; Komárek, J

2013-06-01

299

Sensitivity analysis and calibration of a soil carbon model (SoilGen2) in two contrasting loess forest soils  

NASA Astrophysics Data System (ADS)

To accurately estimate past terrestrial carbon pools is the key to understanding the global carbon cycle and its relationship with the climate system. SoilGen2 is a useful tool to obtain aspects of soil properties (including carbon content) by simulating soil formation processes; thus it offers an opportunity for both past soil carbon pool reconstruction and future carbon pool prediction. In order to apply it to various environmental conditions, parameters related to carbon cycle process in SoilGen2 are calibrated based on six soil pedons from two typical loess deposition regions (Belgium and China). Sensitivity analysis using the Morris method shows that decomposition rate of humus (kHUM), fraction of incoming plant material as leaf litter (frecto) and decomposition rate of resistant plant material (kRPM) are the three most sensitive parameters that would cause the greatest uncertainty in simulated change of soil organic carbon in both regions. According to the principle of minimizing the difference between simulated and measured organic carbon by comparing quality indices, the suited values of kHUM, (frecto and kRPM in the model are deduced step by step and validated for independent soil pedons. The difference of calibrated parameters between Belgium and China may be attributed to their different vegetation types and climate conditions. This calibrated model allows more accurate simulation of carbon change in the whole pedon and has potential for future modeling of carbon cycle over long timescales.

Yu, Y. Y.; Finke, P. A.; Wu, H. B.; Guo, Z. T.

2013-01-01

300

Chitinolyticbacter meiyuanensis SYBC-H1T, gen. nov., sp. nov., a chitin-degrading bacterium isolated from soil.  

PubMed

A novel aerobic mesophilic bacterial strain SYBC-H1(T) capable of degrading chitin was isolated and classified in this study. The strain exhibited strong chitinolytic activity and was a Gram-negative, curved, rod-shaped, and motile bacterium. Growth of this strain was observed between 10 and 41°C and between pH 3.5 and 9.5. The DNA G + C content of strain SYBC-H1(T) was 53.25 mol%. The cellular fatty acids (>5%) were 12:0 iso 3-OH (5.87%), 16:0 (28.16%), and 18:1?7c (20.48%). Phylogenetic analysis based on 16S rRNA gene sequence similarity revealed that strain SYBC-H1(T) belonged to the family Neisseriaceae, and was distantly related (95.0% similarity) to the genus Chitiniphilus. Its phenotype was unique and genetic and phylogenetic analysis experiments suggested that strain SYBC-H1(T) represented the type strain (CGMCC 3438(T), ATCC BAA-2140(T)) of a novel genus, for which the name Chitinolyticbacter meiyuanensis SYBC-H1(T) gen. nov., sp. nov. was proposed. The highest enzymatic activity of chitinase (9.6 U/ml) was obtained at 72 h in 250 ml shake flasks. The 16S rRNA gene sequence of SYBC-H1(T) has been deposited in GenBank under the accession number GQ981314. PMID:21431834

Hao, Zhikui; Cai, Yujie; Liao, Xiangru; Liang, Xiaohui; Liu, Jiayang; Fang, Zhiyou; Hu, Mingming; Zhang, Dabing

2011-06-01

301

Pyramidobacter piscolens gen. nov., sp. nov., a member of the phylum 'Synergistetes' isolated from the human oral cavity  

PubMed Central

Four strains of anaerobic, Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group distinct from any species with validly published names. 16S rRNA and 23S rRNA gene sequence analyses and DNA–DNA reassociation data revealed that the strains constituted a novel group within the phylum ‘Synergistetes’ and were most closely related to Jonquetella anthropi. Two libraries of randomly cloned DNA were prepared from strain W5455T and were sequenced to provide a genome survey as a resource for metagenomic studies. A new genus and novel species, Pyramidobacter piscolens gen. nov., sp. nov., is proposed to accommodate these strains. The genus Pyramidobacter comprises strains that are anaerobic, non-motile, asaccharolytic bacilli that produce acetic and isovaleric acids and minor to trace amounts of propionic, isobutyric, succinic and phenylacetic acids as end products of metabolism. P. piscolens gen. nov., sp. nov. produced hydrogen sulphide but was otherwise largely biochemically unreactive. Growth was stimulated by the addition of glycine to broth media. The G+C content of the DNA of the type strain was 59?mol%. The type strain of Pyramidobacter piscolens sp. nov. is W5455T (=DSM 21147T=CCUG 55836T).

Downes, Julia; Vartoukian, Sonia R.; Dewhirst, Floyd E.; Izard, Jacques; Chen, Tsute; Yu, Wen-Han; Sutcliffe, Iain C.; Wade, William G.

2009-01-01

302

Subulatomonas tetraspora nov. gen. nov. sp. is a member of a previously unrecognized major clade of eukaryotes.  

PubMed

While a large number of aerobic free-living protists have been described within the last decade, the number of new anaerobic or microaerophilic microbial eukaryotic taxa has lagged behind. Here we describe a microaerophilic genus and species of amoeboflagellate isolated from a near-shore marine site off the coast at Plymouth, Massachusetts: Subulatomonas tetraspora nov. gen. nov. sp. This taxon is closely related to Breviata anathema based on both microscopical features and phylogenetic analyses of sequences of three genes: SSU-rDNA, actin, and alpha-tubulin. However, Subulatomonas tetraspora nov. gen. nov. sp. and B. anathema are morphologically distinctive, differ by 14.9% at their SSU-rDNA locus, and were isolated from marine and 'slightly brackish' environments, respectively. Phylogenetic analyses of these two taxa plus closely related sequences from environmental surveys provide support for a novel clade of eukaryotes that is distinct from the major clades including the Opisthokonta, Excavata, Amoebozoa and 'SAR' (Stramenopile, Alveolate, Rhizaria). PMID:21723191

Katz, Laura A; Grant, Jessica; Parfrey, Laura Wegener; Gant, Anastasia; O'Kelly, Charles J; Anderson, O Roger; Molestina, Robert E; Nerad, Thomas

2011-11-01

303

A pipeline of programs for collecting and analyzing group II intron retroelement sequences from GenBank  

PubMed Central

Background Accurate and complete identification of mobile elements is a challenging task in the current era of sequencing, given their large numbers and frequent truncations. Group II intron retroelements, which consist of a ribozyme and an intron-encoded protein (IEP), are usually identified in bacterial genomes through their IEP; however, the RNA component that defines the intron boundaries is often difficult to identify because of a lack of strong sequence conservation corresponding to the RNA structure. Compounding the problem of boundary definition is the fact that a majority of group II intron copies in bacteria are truncated. Results Here we present a pipeline of 11 programs that collect and analyze group II intron sequences from GenBank. The pipeline begins with a BLAST search of GenBank using a set of representative group II IEPs as queries. Subsequent steps download the corresponding genomic sequences and flanks, filter out non-group II introns, assign introns to phylogenetic subclasses, filter out incomplete and/or non-functional introns, and assign IEP sequences and RNA boundaries to the full-length introns. In the final step, the redundancy in the data set is reduced by grouping introns into sets of ?95% identity, with one example sequence chosen to be the representative. Conclusions These programs should be useful for comprehensive identification of group II introns in sequence databases as data continue to rapidly accumulate.

2013-01-01

304

Human GEN1 and the SLX4-associated nucleases MUS81 and SLX1 are essential for the resolution of replication-induced Holliday junctions.  

PubMed

Holliday junctions (HJs), the DNA intermediates of homologous recombination, need to be faithfully processed in order to preserve genome integrity. In human cells, the BLM helicase complex promotes nonnucleolytic dissolution of double HJs. In vitro, HJs may be nucleolytically processed by MUS81-EME1, GEN1, and SLX4-SLX1. Here, we exploit human SLX4-null cells to examine the requirements for HJ resolution in vivo. Lack of BLM and SLX4 or GEN1 and SLX4 is synthetically lethal in the absence of exogenous DNA damage, and lethality is a consequence of dysfunctional mitosis proceeding in the presence of unprocessed HJs. Thus, GEN1 activity cannot be substituted for the SLX4-associated nucleases, and one of the HJ resolvase activities, either of those associated with SLX4 or with GEN1, is required for cell viability, even in the presence of BLM. In vivo HJ resolution depends on both SLX4-associated MUS81-EME1 and SLX1, suggesting that they are acting in concert in the context of SLX4. PMID:24080495

Garner, Elizabeth; Kim, Yonghwan; Lach, Francis P; Kottemann, Molly C; Smogorzewska, Agata

2013-10-17

305

Stages in the Development of Choriopsoropts Kenyensis Gen. et Sp. N. (Acari: Sarcoptiformes: Psoroptidae), A Body Mange Mite from Captive African Buffalo, Syncerus Caffer, in Kenya.  

National Technical Information Service (NTIS)

Stages in the life cycle of Choriopsoroptes kenyensis gen. et. sp. n. are described. The stages for both sexes consist of the egg, larva, protonymph, triponymph, and adult, with the last 3 showing sexual dimorphism. The adult male forms an attachment pair...

G. K. Sweatman J. A. Bindernagel J. B. Walker

1971-01-01

306

Does Therapeutic Equivalence Follow Bioequivalence? A Randomized Trial to Assess Clinical Effects After Switching From Clozaril to Generic Clozapine (Gen-Clozapine)  

Microsoft Academic Search

This study prospectively assessed outcomes in a group of patients who were randomly switched from Clozaril to generic clozapine (Gen-Clozapine). The authors examined data from rating scales administered before the switch and at points after the switch. There were no statistically significant differences between the groups on any baseline measures, including psychiatric status and dose of medication. In the group

Oloruntoba Oluboka; Sandra Stewart; Suzette Landry; Susan Adams

2010-01-01

307

The GenK-catalyzed C-6? Methylation in the Biosynthesis of Gentamicin: Isolation and Characterization of a Cobalamin-dependent Radical SAM Enzyme  

PubMed Central

The existence of cobalamin (Cbl)-dependent enzymes that are members of the radical S-adenosyl-L-methionine (SAM) superfamily was previously predicted based on bioinformatic analysis. A number of these are Cbl-dependent methyltransferases but the details surrounding their reaction mechanisms have remained unclear. In this report we demonstrate the in vitro activity of GenK, a Cbl-dependent radical SAM enzyme that methylates an unactivated sp3 carbon during the biosynthesis of gentamicin, an aminoglycoside antibiotic. Experiments to investigate the stoichiometry of the GenK reaction revealed that one equivalent each of 5?-deoxyadenosine and S-adenosyl-homocysteine are produced for each methylation reaction catalyzed by GenK. Furthermore, isotope-labeling experiments demonstrate that the S-methyl group from SAM is transferred to Cbl and the aminoglycoside product during the course of the reaction. Based on these results, one mechanistic possibility for the GenK reaction can be ruled out and further questions regarding the mechanisms of Cbl-dependent radical SAM methyltransferases, in general, are discussed.

Kim, Hak Joong; McCarty, Reid M.; Ogasawara, Yasushi; Liu, Yung-nan; Mansoorabadi, Steven O.; LeVieux, Jake; Liu, Hung-wen

2013-01-01

308

Detection of Chlamydia trachomatis by the Gen-Probe AMPLIFIED Chlamydia Trachomatis Assay (AMP CT) in Urine Specimens from Men and Women and Endocervical Specimens from Women  

Microsoft Academic Search

Molecular biology-based amplification methods are significantly more sensitive than other methods for the detection of Chlamydia trachomatis. The performance characteristics of the new Gen-Probe AMPLIFIED Chlamydia Trachomatis Assay (AMP CT) with endocervical and urine specimens were compared to those of culture for patients attending two Baltimore City sexually transmitted disease clinics and a clinic for adoles- cents. AMP CT uses

KIMBERLY A. CROTCHFELT; BARBARA PARE; CHARLOTTE GAYDOS; THOMAS C. QUINN

309

Passing of FutureGen: How the World's Premier Clean Coal Technology Project Came to be Abandoned by the Department of Energy.  

National Technical Information Service (NTIS)

When President George W. Bush announced the FutureGen initiative in February of 2003, he described it as a 10-year, $1 billion, government/private partnership to build a coal-based, zero-emissions electricity and hydrogen producing power plant. It would p...

2009-01-01

310

De tec tion of IgE Re ac tiv ity to Fun gus An ti gens by Immunoblotting in Al ler gic Dis eases in Children  

Microsoft Academic Search

Back ground. Fun gi are well-known as sources for al ler gens that cause al ler gic rhi ni - tis and al ler gic asthma. The aim of this study was to eval u ate the prev a lence of sen si - ti za tion to air borne fungi in al ler gic dis eases in chil dren.

Ren-Bin Tang; Horng-Der Shen; Shu-Jen Chen; Ching-Yung Lee

311

The Effects of Lateral Diffusion of Recoil Photoelectrons in Gen.II Image Intensifiers on the Performance of the ACE\\/CRIS Scintillating Optical Fiber Trajectory Detector  

Microsoft Academic Search

It has been observed in Gen. II image intensifiers that a certain fraction of the photoelectrons emitted from the photocathode strike the glass matrix of the front micro-channel plate. These photoelectrons recoil with a distribution of lateral momenta, resulting in a diffusion of the electrons from their original incident position. When used with scintillating fibers, this can result in an

Jennifer Fues; W. R. Binns; Paul L. Hink; Kim Slavis; D. H. Kaplan

1996-01-01

312

Amorosia littoralis gen. sp. nov., a new genus and species name for the scorpinone and caffeine-producing hyphomycete from the littoral zone in The Bahamas  

Microsoft Academic Search

The new generic and species name Amorosia littoralis gen. sp. nov. is introduced for the conidial dematiaceous hyphomycete isolated from the littoral zone in The Bahamas and reported in 2001 to produce the novel aza-anthraquinone scorpinone, and also caffeine. No satisfactory generic placement was found at the time, but subsequent morphological and molecular investigations reveal that a new generic name

Peter G. Mantle; David L. Hawksworth; Sylvie Pazoutova; Lucy M. Collinson; Birgitte R. Rassing

2006-01-01

313

Novel chemolithotrophic, thermophilic, anaerobic bacteria Thermolithobacter ferrireducens gen. nov., sp. nov. and Thermolithobacter carboxydivorans sp. nov.  

PubMed

Three thermophilic strains of chemolithoautotrophic Fe(III)-reducers were isolated from mixed sediment and water samples (JW/KA-1 and JW/KA-2(T): Calcite Spring, Yellowstone N.P., WY, USA; JW/JH-Fiji-2: Savusavu, Vanu Levu, Fiji). All were Gram stain positive rods (approximately 0.5 x 1.8 microm). Cells occurred singly or in V-shaped pairs, and they formed long chains in complex media. All utilized H(2) to reduce amorphous iron (III) oxide/hydroxide to magnetite at temperatures from 50 to 75 degrees C (opt. approximately 73 degrees C). Growth occurred within the pH(60C) range of 6.5-8.5 (opt. pH(60C) 7.1-7.3). Magnetite production by resting cells occurred at pH(60C) 5.5-10.3 (opt. 7.3). The iron (III) reduction rate was 1.3 mumol Fe(II) produced x h(-1) x ml(-1) in a culture with 3 x 10(7) cells, one of the highest rates reported. In the presence or absence of H(2), JW/KA-2(T) did not utilize CO. The G + C content of the genomic DNA of the type strain is 52.7 +/- 0.3 mol%. Strains JW/KA-1 and JW/KA-2(T) each contain two different 16S rRNA gene sequences. The 16S rRNA gene sequences from JW/KA-1, JW/KA-2(T), or JW/JH-Fiji-2 possessed >99% similarity to each other but also 99% similarity to the 16S rRNA gene sequence from the anaerobic, thermophilic, hydrogenogenic CO-oxidizing bacterium 'Carboxydothermus restrictus' R1. DNA-DNA hybridization between strain JW/KA-2(T) and strain R1(T) yielded 35% similarity. Physiological characteristics and the 16S rRNA gene sequence analysis indicated that the strains represent two novel species and are placed into the novel genus Thermolithobacter within the phylum 'Firmicutes'. In addition, the levels of 16S rRNA gene sequence similarity between the lineage containing the Thermolithobacter and well-established members of the three existing classes of the 'Firmicutes' is less than 85%. Therefore, Thermolithobacter is proposed to constitute the first genus within a novel class of the 'Firmicutes', Thermolithobacteria. The Fe(III)-reducing Thermolithobacter ferrireducens gen. nov., sp. nov. is designated as the type species with strain JW/KA-2(T) (ATCC 700985(T), DSM 13639(T)) as its type strain. Strain R1(T) is the type strain for the hydrogenogenic, CO-oxidizing Thermolithobacter carboxydivorans sp. nov. (DSM 7242(T), VKM 2359(T)). PMID:17021657

Sokolova, T; Hanel, J; Onyenwoke, R U; Reysenbach, A-L; Banta, A; Geyer, R; González, J M; Whitman, W B; Wiegel, J

2007-01-01

314

Pontibacter actiniarum gen. nov., sp. nov., a novel member of the phylum 'Bacteroidetes', and proposal of Reichenbachiella gen. nov. as a replacement for the illegitimate prokaryotic generic name Reichenbachia Nedashkovskaya et al. 2003.  

PubMed

The taxonomic position of a marine, gliding, pink-pigmented, aerobic, heterotrophic and Gram-negative bacterium was established using a polyphasic approach. 16S rRNA gene sequence analysis indicated that the strain was a member of the phylum 'Bacteroidetes' in which it occupied a separate lineage. The predominant cellular fatty acids were C15 : 0 iso, C17 : 0 iso 3-OH, summed feature 3 and summed feature 4. The DNA G+C content was 48.7 mol%. Phylogenetic evidence and the results of phenotypic, genotypic and chemotaxonomic analyses strongly support the assignment of the newly isolated bacterium as a member of a novel genus and species, for which the name Pontibacter actiniarum gen. nov., sp. nov. is proposed. The type strain is KMM 6156T (=KCTC 12367T=LMG 23027T). It is also proposed that the illegitimate names Reichenbachia and Reichenbachia agariperforans are replaced with Reichenbachiella and Reichenbachiella agariperforans, respectively. PMID:16280531

Nedashkovskaya, Olga I; Kim, Seung Bum; Suzuki, Makoto; Shevchenko, Lyudmila S; Lee, Myung Sook; Lee, Kang Hyun; Park, Myung Soo; Frolova, Galina M; Oh, Hyun Woo; Bae, Kyung Sook; Park, Ho-Yong; Mikhailov, Valery V

2005-11-01

315

Carboxylicivirga gen. nov. in the family Marinilabiliaceae with two novel species, Carboxylicivirga mesophila sp. nov. and Carboxylicivirga taeanensis sp. nov., and reclassification of Cytophaga fermentans as Saccharicrinis fermentans gen. nov., comb. nov.  

PubMed

Two facultatively anaerobic mesophilic bacteria, strains MEBiC 07026(T) and MEBiC 08903(T), were isolated from two different tidal flat sediments and both strains showed approximately 92.2?% 16S rRNA gene sequence similarity with [Cytophaga] fermentans DSM 9555(T). 16S rRNA gene sequence similarity between the two new isolates was 97.5?% but levels of DNA-DNA relatedness between the two were 31.3-31.8?%. Phylogenetic analysis revealed that the two isolates and [Cytophaga] fermentans DSM 9555(T) were affiliated with the family Marinilabiliaceae in the class Bacteroidia. The dominant fatty acids of strains MEBiC 07026(T), MEBiC 08903(T) and [Cytophaga] fermentans DSM 9555(T) were branched-type or hydroxylated C15?:?0, but [Cytophaga] fermentans DSM 9555(T) contained a higher proportion of anteiso-branched fatty acids. The two new isolates contained a markedly higher proportion of monounsaturated fatty acids than other members of the family Marinilabiliaceae. The major respiratory quinone of the strains was MK-7. Strains MEBiC07026(T) and MEBiC08903(T) utilized a wide range of carboxylic acids whereas [Cytophaga] fermentans DSM 9555(T) utilized carbohydrates rather than carboxylic acids. The DNA G+C content of the novel strains was about 44 mol% but that of [Cytophaga] fermentans DSM 9555(T) revealed from the genome sequence was 37.6 mol%. Based on evidence from this polyphasic taxonomic study, a novel genus, Carboxylicivirga gen. nov., is proposed in the family Marinilabiliaceae with two novel species, Carboxylicivirga mesophila sp. nov. with type strain MEBiC 07026(T) (?=?KCCM 42978(T)?=?JCM 18290(T)) and Carboxylicivirga taeanensis sp. nov. with type strain MEBiC 08903(T) (?=?KCCM 43024(T)?=?JCM 19490(T)). Additionally, [Cytophaga] fermentans DSM 9555(T) (?=?ATCC 19072(T)) is reclassified as Saccharicrinis fermentans gen. nov., comb. nov. PMID:24436065

Yang, Sung-Hyun; Seo, Hyun-Seok; Woo, Jung-Hee; Oh, Hyun-Myung; Jang, Hani; Lee, Jung-Hyun; Kim, Sang-Jin; Kwon, Kae Kyoung

2014-04-01

316

Novel members of the family Flavobacteriaceae from Antarctic maritime habitats including Subsaximicrobium wynnwilliamsii gen. nov., sp. nov., Subsaximicrobium saxinquilinus sp. nov., Subsaxibacter broadyi gen. nov., sp. nov., Lacinutrix copepodicola gen. nov., sp. nov., and novel species of the genera Bizionia, Gelidibacter and Gillisia.  

PubMed

Several orange- and yellow-pigmented, halophilic, strictly aerobic, chemoheterotrophic, Gram-negative strains were isolated during investigations of maritime Antarctic habitats, including coastal fast sea-ice brine and algae, crustaceans and quartz stone sublithic cyanobacterial biofilms. Isolates investigated in this study belonged to the marine clade of the family Flavobacteriaceae and represented lineages that were either distinct from species with validly published names or appeared to be distinct species within existing genera. A polyphasic taxonomic analysis demonstrated the novelty of these strains, and several new taxa are proposed. Strains from quartz stone sublithic communities were grouped into two new genera designated Subsaximicrobium gen. nov. and Subsaxibacter gen. nov. The genus Subsaximicrobium included the species Subsaximicrobium wynnwilliamsii sp. nov. (type species; type strain G#7(T)=ACAM 1070(T)=CIP 108525(T)) and Subsaximicrobium saxinquilinus sp. nov. (type strain Y4-5(T)=ACAM 1063(T)=CIP 108526(T)). The genus Subsaxibacter contained a single species designated Subsaxibacter broadyi sp. nov. (type strain P7(T)=ACAM 1064(T)=CIP 108527(T)). A novel bacterial strain isolated from the lake-dwelling, calanoid copepod Paralabidocera antarctica was given the name Lacinutrix copepodicola gen. nov., sp. nov. (type strain DJ3(T)=ACAM 1055(T)=CIP 108538(T)). Four novel species of the genus Bizionia were discovered, Bizionia algoritergicola sp. nov. (type strain APA-1(T)=ACAM 1056(T)=CIP 108533(T)) and Bizionia myxarmorum sp. nov. (type strain ADA-4(T)=ACAM 1058(T)=CIP 108535(T)), which were isolated from the carapace surfaces of sea-ice algae-feeding amphipods, and Bizionia gelidisalsuginis sp. nov. (type strain IC164(T)=ACAM 1057(T)=CIP 108536(T)) and Bizionia saleffrena sp. nov. (type strain HFD(T)=ACAM 1059(T)=CIP 108534(T)), which were isolated from sea-ice brines. Several other novel species were also isolated from sea-ice samples, including two novel species of the genus Gelidibacter, Gelidibacter gilvus sp. nov. (type strain IC158(T)=ACAM 1054(T)=CIP 108531(T)) and Gelidibacter salicanalis sp. nov. (type strain IC162(T)=ACAM 1053(T)=CIP 108532(T)), as well as three novel species of the genus Gillisia, Gillisia illustrilutea sp. nov. (type strain IC157(T)=ACAM 1062(T)=CIP 108530(T)), Gillisia sandarakina sp. nov. (type strain IC148(T)=ACAM 1060(T)=CIP 108529(T)) and Gillisia hiemivivida sp. nov. (type strain IC154(T)=ACAM 1061(T)=CIP 108528(T)). PMID:16014468

Bowman, John P; Nichols, David S

2005-07-01

317

Experimental Investigations of the Ablation of Wire Arrays on the 250 kA GenASIS Machine  

NASA Astrophysics Data System (ADS)

We present investigations of exploding wire experiments on a recently completed linear transformer driver (LTD) in the High Energy Density Physics laboratory at UCSD. The GenASIS machine delivers >250kA in 130ns to short circuit and >200kA to a wire array load, via a conical constant gap power feed. Measured load currents compare favorably to circuit modeling. This new generator facilitates ablation studies of multiple wire cylindrical arrays with >25 kA/ wire, and we present laser Schlieren imaging, along with radial and axial electron density profiles inferred from interferometry for Al and W arrays, which are compared to analytical theory. In addition, conical wire arrays are used to generate supersonic plasma jets. We present characterization of high atomic number jets along with estimates of the local sound speed and Mach number.

Bott, S. C.; Haas, D. M.; Eshaq, Y.; Ueda, U.; Madden, R. E.; Collins, G.; Beg, F. N.

2008-11-01

318

Effect of hydrostatic pressure on the band-gap luminescence of strain-adjusted SimGen superlattices  

NASA Astrophysics Data System (ADS)

We report an experimental study of the band-gap photoluminescence from strain-adjusted SimGen (m=9,6,3; n=6,4,2) superlattices under applied hydrostatic pressure. The strain adjustment was achieved by a thick, step-graded Si1-xGex buffer layer resulting in an improved quality of the superlattice with respect to dislocation density. The no-phonon (NP) lines shift linearly under applied hydrostatic pressure in all superlattices to lower energies. The stress dependence was modeled using an approach based on deformation potentials and effective-mass theory. Under the assumptions made a close resemblance between experiment and theory was found. From the slopes of the stress shifts and amplitudes under various pressures, further evidence is given to an earlier assignment of the NP lines as arising from band-to-band recombination.

Olajos, Janos; Jia, Ying-Bo; Engvall, Jesper; Grimmeiss, Hermann G.; Kasper, Erich; Kibbel, Horst; Presting, Hartmut

1994-01-01

319

Advenella incenata gen. nov., sp. nov., a novel member of the Alcaligenaceae, isolated from various clinical samples.  

PubMed

A polyphasic taxonomic study of 14 isolates recovered from various human and veterinary clinical samples was performed. Phenotypically these isolates shared several characteristics with members of the Alcaligenaceae and related genera. Random amplified polymorphic DNA fingerprinting and whole-cell protein analysis suggested the presence of multiple genomic groups, which was confirmed by DNA-DNA hybridization experiments. 16S rRNA gene sequence analysis indicated that these isolates were related to the genera Pelistega, Taylorella, Oligella, Pigmentiphaga, Alcaligenes, Kerstersia, Achromobacter and Bordetella and belonged to the family Alcaligenaceae. Based on the results of the present study the organisms were classified in a novel genus, Advenella gen. nov. This genus comprises one named species, Advenella incenata sp. nov. (type strain LMG 22250T=CCUG 45225T) and five currently unnamed genomic species. The DNA G+C content of members of the novel genus Advenella is between 54.0 and 57.7 mol%. PMID:15653883

Coenye, Tom; Vanlaere, Elke; Samyn, Emly; Falsen, Enevold; Larsson, Peter; Vandamme, Peter

2005-01-01

320

Larkinella insperata gen. nov., sp. nov., a bacterium of the phylum 'Bacteroidetes' isolated from water of a steam generator.  

PubMed

A Gram-negative bacterium, designated strain LMG 22510T, was isolated from water of a pharmaceutical company steam generator. The cells had a ring-like and horseshoe-shaped morphology and possessed gliding motility. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain was a member of the Flexibacter group within the phylum 'Bacteroidetes'; its nearest neighbour was Spirosoma linguale (88.8 % sequence similarity). DNA base content, fatty acid composition and biochemical characteristics were determined. Genotypic and phenotypic data indicated that strain LMG 22510T could not be assigned to any recognized genus; therefore, a novel genus and species is proposed, Larkinella insperata gen. nov., sp. nov., with LMG 22510T (= NCIMB 14103T) as the type strain. PMID:16403892

Vancanneyt, Marc; Nedashkovskaya, Olga I; Snauwaert, Cindy; Mortier, Stefanie; Vandemeulebroecke, Katrien; Hoste, Bart; Dawyndt, Peter; Frolova, Galina M; Janssens, Danielle; Swings, Jean

2006-01-01

321

Trilosporoides platessae gen. et sp. n. (Myxozoa: Multivalvulida) in the plaice Pleuronectes platessa (Teleostei: Pleuronectidae) from Denmark.  

PubMed

A new myxosporean species, Trilosporoides platessae gen. et sp. n. (Multivalvulida), is described from the gallbladder of the plaice Pleuronectes platessa L. (Pleuronectidae) from Denmark. The myxospore of T. platessae is conical in side view, with a 24 microm long, pointed posterior projection. In apical view, the myxospore (diameter 9.4 microm) is round, trilobed and with three spherical polar capsules arranged peripherally, equidistant and opening peripherally through protruding tips. The polar capsules are of different sizes, one often larger than the others (diameter 3.3 microm vs. 2.5 microm). Apart from the long posterior projection, the myxospore of T. platessae differs from those of the three known species of Trilospora Noble, 1959 and from all genera within the order Multivalvulida Shulman, 1959 in the arrangement of the polar capsules. Trilosporoides platessae may temporarily be placed in the vicinity of the Trilosporidae. PMID:16405293

Køie, Marianne

2005-11-01

322

Draconibacterium orientale gen. nov., sp. nov., isolated from two distinct marine environments, and proposal of Draconibacteriaceae fam. nov.  

PubMed

The taxonomic characteristics of two bacterial strains, FH5T and SS4, isolated from enrichment cultures obtained from two distinct marine environments, were determined. These bacteria were Gram-stain-negative, facultatively anaerobic rods. Growth occurred at 20-40 °C (optimum, 28-32 °C), pH 5.5-9.0 (optimum, pH 7.0-7.5) and in the presence of 1-7% NaCl (optimum, 2-4%). The major cellular fatty acids were anteiso-C15:0 and iso-C15:0. Menaquinone 7 (MK-7) was the sole respiratory quinone. The major polar lipids were phosphatidylethanolamine, an unkown phospholipid and an unknown lipid. The DNA G+C contents of strains FH5T and SS4 were both determined to be 42.0?mol%. The results of DNA-DNA hybridization studies indicated that the FH5T and SS4 genomes share greater than 95% relatedness. The strains formed a distinct phyletic line within the class Bacteroidia, with less than 89.4% sequence similarity to their closest relatives with validly published names. On the basis of physiological and biochemical characteristics, 16S rRNA gene sequences and chemical properties, a novel genus and species, Draconibacterium orientale gen. nov., sp. nov., within the class Bacteroidia, are proposed, with strain FH5T (=DSM 25947T=CICC 10585T) as the type strain. In addition, a new family, Draconibacteriaceae fam. nov., is proposed to accommodate Draconibacterium gen. nov. PMID:24523447

Du, Zong-Jun; Wang, Ying; Dunlap, Christopher; Rooney, Alejandro P; Chen, Guan-Jun

2014-05-01

323

Endozoicomonas elysicola gen. nov., sp. nov., a gamma-proteobacterium isolated from the sea slug Elysia ornata.  

PubMed

A Gram-negative, strictly aerobic, rod-formed bacterium, strain MKT110(T), was isolated from a mollusk, the sea slug Elysia ornata collected in seawater off the coast of Izu-Miyake Island, Japan at a depth of 15m. Comparative 16S rRNA gene sequences analysis indicated that the isolate MKT110(T) constituted a novel lineage in gamma-proteobacteria related to the genera Zooshikella, Oceanospirillum, Microbulbifer, Marinobacter, Saccharospirillum and Pseudomonas. The strain MKT110(T) was closely related to the clones from marine sponge Halichondria okadai (AB054136, AB054161) and the coral Pocillopora damicornis (AY700600, AY700601). The phylogenetic tree based on the 16S rRNA gene sequences showed that MKT110(T) and four clones formed a sub-lineage related to the genus Zooshikella, with a bootstrap value of 100%. MKT110(T) required salt for its growth and was mesophilic. The bacterium contained 16:1omega7c, 16:0 and 14:0 as major cellular fatty acids, and 3-OH 14:0, 3-OH 10:0 and 3-OH 12:0 as major hydroxy fatty acids. The DNA base composition of the isolate was 50.4 mol% G+C. The major quinone was Q-9. The bacterium is distinguished from currently recognized bacterial genera based on phylogenetic and phenotypic features and should be classified in a novel genus for which the name Endozoicomonas elysicola gen. nov., sp. nov. is proposed. (type strain MKT110(T)=IAM 15107(T)=KCTC 12372(T); GenBank accession no. AB196667). PMID:16904280

Kurahashi, Midori; Yokota, Akira

2007-04-01

324

Enhanced/Synthetic Vision and Head-Worn Display Technologies for Terminal Maneuvering Area NextGen Operations  

NASA Technical Reports Server (NTRS)

NASA is researching innovative technologies for the Next Generation Air Transportation System (NextGen) to provide a "Better-Than-Visual" (BTV) capability as adjunct to "Equivalent Visual Operations" (EVO); that is, airport throughputs equivalent to that normally achieved during Visual Flight Rules (VFR) operations rates with equivalent and better safety in all weather and visibility conditions including Instrument Meteorological Conditions (IMC). These new technologies build on proven flight deck systems and leverage synthetic and enhanced vision systems. Two piloted simulation studies were conducted to access the use of a Head-Worn Display (HWD) with head tracking for synthetic and enhanced vision systems concepts. The first experiment evaluated the use a HWD for equivalent visual operations to San Francisco International Airport (airport identifier: KSFO) compared to a visual concept and a head-down display concept. A second experiment evaluated symbology variations under different visibility conditions using a HWD during taxi operations at Chicago O'Hare airport (airport identifier: KORD). Two experiments were conducted, one in a simulated San Francisco airport (KSFO) approach operation and the other, in simulated Chicago O'Hare surface operations, evaluating enhanced/synthetic vision and head-worn display technologies for NextGen operations. While flying a closely-spaced parallel approach to KSFO, pilots rated the HWD, under low-visibility conditions, equivalent to the out-the-window condition, under unlimited visibility, in terms of situational awareness (SA) and mental workload compared to a head-down enhanced vision system. There were no differences between the 3 display concepts in terms of traffic spacing and distance and the pilot decision-making to land or go-around. For the KORD experiment, the visibility condition was not a factor in pilot's rating of clutter effects from symbology. Several concepts for enhanced implementations of an unlimited field-of-regard BTV concept for low-visibility surface operations were determined to be equivalent in pilot ratings of efficacy and usability.

Arthur, Jarvis J., III; Prinzell, Lawrence J.; Williams, Steven P.; Bailey, Randall E.; Shelton, Kevin J.; Norman, R. Mike

2011-01-01

325

GenLab: A MATLAB ®-based program for structural analysis of folds mapped by GPS or seismic methods  

NASA Astrophysics Data System (ADS)

GenLab is a MATLAB ® code for structural analysis of digitally and seismically mapped horizons based on the geometrical model of the developable surface. This model is chosen because surfaces of this type result from the bending of a non-stretching stratum and because deviation from developable geometry implies that bed stretching during folding has occurred. The model is therefore linked with straining of the horizon and can be used for highlighting regions of deformation expressed by brittle fracturing or ductile deformation. Mathematically, a developable surface is one upon which straight lines (generators) can be drawn, and along these generators the orientations of tangent planes of the surface remain constant. Our method involves treating real geological surfaces as approximations to developable surfaces and determines the generator lines at different points on the surface. At these points we consider strip samples of the surface radiating in different directions and examine the variability of strike and dip within each sample strip. The radial scan-line length parameter is user-defined, and the optimal value can be easily identified by geostatistical analysis of the depth data. The local plunge lines (the approximation to the generatrix of a developable fold) are therefore identified as the direction associated with the least variation of surface attitude, i.e., the most constant strike and dip. The map pattern obtained by analyzing the plunges and trends of plunge lines across an area allows identification of domains where folding accords closely with a developable geometry. Such domains are recognized from straight plunge lines, defining parallel or convergent patterns. According to the model, deviations from these patterns correspond to regions of structural complexity associated with ductile or brittle straining of the surface being analyzed. The plunge-line analysis therefore offers a useful technique with potential for predicting strained zones and automatic fault recognition. GenLab allows the rapid implementation of this analysis and uses the matrix capabilities and contouring functions of MATLAB.

Fernández-Martínez, J. L.; Lisle, Richard J.

2009-02-01

326

Enhanced/synthetic vision and head-worn display technologies for terminal maneuvering area NextGen operations  

NASA Astrophysics Data System (ADS)

NASA is researching innovative technologies for the Next Generation Air Transportation System (NextGen) to provide a "Better-Than-Visual" (BTV) capability as adjunct to "Equivalent Visual Operations" (EVO); that is, airport throughputs equivalent to that normally achieved during Visual Flight Rules (VFR) operations rates with equivalent and better safety in all weather and visibility conditions including Instrument Meteorological Conditions (IMC). These new technologies build on proven flight deck systems and leverage synthetic and enhanced vision systems. Two piloted simulation studies were conducted to access the use of a Head-Worn Display (HWD) with head tracking for synthetic and enhanced vision systems concepts. The first experiment evaluated the use a HWD for equivalent visual operations to San Francisco International Airport (airport identifier: KSFO) compared to a visual concept and a head-down display concept. A second experiment evaluated symbology variations under different visibility conditions using a HWD during taxi operations at Chicago O'Hare airport (airport identifier: KORD). Two experiments were conducted, one in a simulated San Francisco airport (KSFO) approach operation and the other, in simulated Chicago O'Hare surface operations, evaluating enhanced/synthetic vision and head-worn display technologies for NextGen operations. While flying a closely-spaced parallel approach to KSFO, pilots rated the HWD, under low-visibility conditions, equivalent to the out-the-window condition, under unlimited visibility, in terms of situational awareness (SA) and mental workload compared to a head-down enhanced vision system. There were no differences between the 3 display concepts in terms of traffic spacing and distance and the pilot decision-making to land or go-around. For the KORD experiment, the visibility condition was not a factor in pilot's rating of clutter effects from symbology. Several concepts for enhanced implementations of an unlimited field-of-regard BTV concept for low-visibility surface operations were determined to be equivalent in pilot ratings of efficacy and usability.

Arthur, Jarvis J., III; Prinzel, Lawrence J., III; Williams, Steven P.; Bailey, Randall E.; Shelton, Kevin J.; Norman, R. Mike

2011-05-01

327

Description of Thalassotalea piscium gen. nov., sp. nov., isolated from flounder (Paralichthys olivaceus), reclassification of four species of the genus Thalassomonas as members of the genus Thalassotalea gen. nov. and emended description of the genus Thalassomonas.  

PubMed

A Gram-staining-negative, aerobic, rod-shaped bacterium, designated strain T202(T), was isolated from the gill of a cultured flounder (Paralichthys olivaceus). Based on 16S rRNA gene sequence similarity, strain T202(T) was a member of the family Colwelliaceae and shared 93.32-96.58?% similarity with type strains of all members of the most closely related genus Thalassomonas. Phylogenetically, the isolate shared a root with the type strains of four marine species, Thalassomonas agariperforans M-M1(T), Thalassomonas agarivorans TMA1(T), Thalassomonas loyana CBMAI 722(T) and Thalassomonas ganghwensis JC2041(T). Optimal growth occurred in the presence of 2-4?% (w/v) NaCl, at pH 7.0-8.0 and at 28 °C. Ubiquinone 8 (Q-8) was the predominant respiratory quinone. The major fatty acids were C16?:?0, summed feature 3 (C16?:?1?7c and/or C16?:?1?6c), C16?:?1?9c and C17?:?1?8c. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain T202(T) was 37 mol%. On the basis of polyphasic analysis, especially the phylogenetic relationships and the lower DNA G+C content, strain T202(T) is considered to represent a novel species in a new genus, for which the name Thalassotalea piscium gen. nov., sp. nov. is proposed. The type strain of Thalassotalea piscium is T202(T) (?=?JCM 18590(T)?=?DSM 26287(T)?=?KCTC 32144(T)). Because Thalassomonas agariperforans M-M1(T), Thalassomonas agarivorans TMA1(T), Thalassomonas loyana CBMAI 722(T) and Thalassomonas ganghwensis JC2041(T) formed a phylogenetic group together with strain T202(T) that was clearly separated from other known strains of Thalassomonas, these four species are reclassified as members of the genus Thalassotalea as Thalassotalea agariperforans comb. nov. (type strain M-M1(T)?=?KCTC 23343(T)?=?CCUG 60020(T)), Thalassotalea agarivorans comb. nov. (type strain TMA1(T)?=?BCRC 17492(T)?=?JCM 13379(T)?=?DSM 19706(T)), Thalassotalea loyana comb. nov. (type strain CBMAI 722(T)?=?LMG 22536(T)) and Thalassotalea ganghwensis comb. nov. (type strain JC2041(T)?=?IMSNU 14005(T)?=?KCTC 12041(T)?=?DSM 15355(T)). The type species of the genus Thalassotalea is Thalassotalea ganghwensis gen. nov., comb. nov. An emended description of the genus Thalassomonas is also proposed. PMID:24421274

Zhang, Yunhui; Tang, Kaihao; Shi, Xiaochong; Zhang, Xiao-Hua

2014-04-01

328

Description of Niveispirillum fermenti gen. nov., sp. nov., isolated from a fermentor in Taiwan, transfer of Azospirillum irakense (1989) as Niveispirillum irakense comb. nov., and reclassification of Azospirillum amazonense (1983) as Nitrospirillum amazonense gen. nov.  

PubMed

A taxonomic study was carried out on a novel aerobic bacterial strain (designated CC-LY736(T)) isolated from a fermentor in Taiwan. Cells of strain CC-LY736(T) were Gram-stain negative, spiral-shaped and motile by means of a monopolar flagellum. Strain CC-LY736(T) shared the greatest degree of 16S rRNA gene sequence similarity to Azospirillum irakense DSM 11586(T) (97.2 %), Rhodocista centenaria JCM 21060(T) (96.3 %) and Rhodocista pekingensis JCM 11669(T) (96.1 %). The major fatty acids were C16:0, C16:1 ?5c, C19:0 cyclo ?8c, C18:1 ?7c/C18:1 ?6c, C16:0 3-OH and C18:1 2-OH. The predominant polar lipids included phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidyldimethylethanolamine and two unidentified glycolipids. The common major respiratory quinone was ubiquinone Q-10 and predominant polyamines were sym-homospermidine and putrescine. The DNA G+C content of strain CC-LY736(T) was 67.6 ± 0.1 mol %. During phylogenetic analysis, strain CC-LY736(T) formed a unique phyletic lineage associated with Rhodocista species. However, the combination of genetic, chemotaxonomic and physiological data clearly indicated that strain CC-LY736(T) was a novel representative of the family Rhodospirillaceae. Based on the polyphasic comparison, the name Niveispirillum fermenti gen. nov., sp. nov. is proposed; the type strain of the type species is CC-LY736(T) (= BCRC 80504(T) = LMG 27263(T)). In addition, the reclassifications of Azospirillum irakense as Niveispirillum irakense comb. nov. (type strain KBC1(T) = ATCC 51182(T) = BCRC 15764(T) = CIP 103311(T)), and Azospirillum amazonense as Nitrospirillum amazonense gen. nov., sp. nov. (type strain Am14(T) = ATCC 35119(T) = BCRC 14279(T) = DSM 3787(T)) are proposed based on the polyphasic taxonomic data obtained in this study. PMID:24771126

Lin, Shih-Yao; Hameed, Asif; Shen, Fo-Ting; Liu, You-Cheng; Hsu, Yi-Han; Shahina, Mariyam; Lai, Wei-An; Young, Chiu-Chung

2014-06-01

329

Boltimys broomi gen. nov., sp. nov. (Rodentia, Mammalia), nouveau Muridae d'affinité incertaine du Pliocène inférieur d'Afrique du Sud  

NASA Astrophysics Data System (ADS)

Boltimys broomi gen. nov., sp. nov., a Muridae of uncertain affinity in the Early Pliocene of South Africa. Boltimys broomi gen. nov., sp. nov. is reported from the Early Pliocene fauna of Waypoint 160, a fossiliferous locality in the area of Bolt's Farm (Province of Gauteng) near Krugersdorp in South Africa. The occlusal surface of the jugal teeth is characterized by a basin-shaped aspect due to the coalescence of the cusps which make the lobes of the molars. An accessory inner cusp is present on the first and second upper molars. A faint longitudinal crest is present only in the first lower molar. The new rodent is tentatively referred to the subfamily Myocricetodontinae.

Sénégas, Frank; Michaux, Jacques

2000-04-01

330

Effect of Type 2 Diabetes Mellitus on Left Ventricular Geometry and Systolic Function in Hypertensive Subjects Hypertension Genetic Epidemiology Network (HyperGEN) Study  

Microsoft Academic Search

Background—Type 2 diabetes is a cardiovascular risk factor. It remains to be elucidated in a large, population-based sample whether diabetes is associated with changes in left ventricular (LV) structure and systolic function independent of obesity and systolic blood pressure (BP). Methods and Results—Among 1950 hypertensive participants in the HyperGEN Study without overt coronary heart disease or significant valve disease, 20%

Vittorio Palmieri; Jonathan N. Bella; Donna K. Arnett; Jennifer E. Liu; Albert Oberman; Min-Yan Schuck; Dalane W. Kitzman; Paul N. Hopkins; Derek Morgan; D. C. Rao; Richard B. Devereux

331

A new genus of oak gallwasp, Coffeikokkos Pujade-Villar & Melika, gen. n., with a description of a new species from Costa Rica (Hymenoptera, Cynipidae)  

PubMed Central

Abstract A new genus of oak gallwasp, Coffeikokkos Pujade-Villar & Melika, gen. n., is described from Costa Rica. Diagnostic characters and generic limits of the new genus are discussed in detail. The new genus includes Coffeikokkos copeyensis Pujade-Villar & Melika, sp. n., which induces galls on stems of Quercus bumelioides, an endemic oak to Costa Rica, Honduras and Panama. The new species and galls are described and illustrated.

Pujade-Villar, Juli; Hanson, Paul; Melika, George

2012-01-01

332

A new approach for GenCos profit based unit commitment in day-ahead competitive electricity markets considering reserve uncertainty  

Microsoft Academic Search

This paper presents a new approach for GenCos Profit Based Unit Commitment (GPBUC) in day-ahead competitive electricity markets. Generation, spinning and non-spinning reserves are considered in the proposed formulation. The estimated probability that spinning and non-spinning reserves are called and generated is also considered in the formulation to simulate the reserve uncertainty. The artificial neural network (ANN) is applied for

H. Y. Yamin; Q. El-Dwairi; S. M. Shahidehpour

2007-01-01

333

Iodination with Iodo-Gen and Radioimmunoassay of Cholecystokinin (CCK) in Acidified Plasma, CCK Release, and Molecular CCK Components in Man  

Microsoft Academic Search

The preparation of a stable fully immunoreactive 125I-labeled CCK39 using a modified Iodo-gen method with high specific radioactivity; the production of an avid and specific cholecystokinin (CCK) antiserum, and a sensitive, precise and specific radioimmunoassay method allowing measurements of fasting plasma CCK in the low picomole per liter range together with the significant rises in plasma CCK following a test

P. G. Burhol; T. G. Jenssen; I. Lygren; T. B. Schulz; R. Jorde; H. L. Waldum

1982-01-01

334

GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords  

PubMed Central

Background Biomedical researchers often want to explore pathogenesis and pathways regulated by abnormally expressed genes, such as those identified by microarray analyses. Literature mining is an important way to assist in this task. Many literature mining tools are now available. However, few of them allows the user to make manual adjustments to zero in on what he/she wants to know in particular. Results We present our software program, GenCLiP (Gene Cluster with Literature Profiles), which is based on the methods presented by Chaussabel and Sher (Genome Biol 2002, 3(10):RESEARCH0055) that search gene lists to identify functional clusters of genes based on up-to-date literature profiling. Four features were added to this previously described method: the ability to 1) manually curate keywords extracted from the literature, 2) search genes and gene co-occurrence networks related to custom keywords, 3) compare analyzed gene results with negative and positive controls generated by GenCLiP, and 4) calculate probabilities that the resulting genes and gene networks are randomly related. In this paper, we show with a set of differentially expressed genes between keloids and normal control, how implementation of functions in GenCLiP successfully identified keywords related to the pathogenesis of keloids and unknown gene pathways involved in the pathogenesis of keloids. Conclusion With regard to the identification of disease-susceptibility genes, GenCLiP allows one to quickly acquire a primary pathogenesis profile and identify pathways involving abnormally expressed genes not previously associated with the disease.

Huang, Zhong-Xi; Tian, Hui-Yong; Hu, Zhen-Fu; Zhou, Yi-Bo; Zhao, Jin; Yao, Kai-Tai

2008-01-01

335

Acidicapsa borealis gen. nov., sp. nov. and Acidicapsa ligni sp. nov., subdivision 1 Acidobacteria from Sphagnum peat and decaying wood.  

PubMed

Two strains of subdivision 1 Acidobacteria, a pink-pigmented bacterium KA1(T) and a colourless isolate WH120(T), were obtained from acidic Sphagnum peat and wood under decay by the white-rot fungus Hyploma fasciculare, respectively. Cells of these isolates were Gram-negative-staining, non-motile, short rods, which were covered by large polysaccharide capsules and occurred singly, in pairs, or in short chains. Strains KA1(T) and WH120(T) were strictly aerobic mesophiles that grew between 10 and 33 °C, with an optimum at 22-28 °C. Both isolates developed under acidic conditions, but strain WH120(T) was more acidophilic (pH growth range 3.5-6.4; optimum, 4.0-4.5) than strain KA1(T) (pH growth range 3.5-7.3; optimum , 5.0-5.5). The preferred growth substrates were sugars. In addition, the wood-derived isolate WH120(T) grew on oxalate, lactate and xylan, while the peat-inhabiting acidobacterium strain KA1(T) utilized galacturonate, glucuronate and pectin. The major fatty acids were iso-C(15:0) and iso-C(17:1)?8c; the cells also contained significant amounts of 13,16-dimethyl octacosanedioic acid. The quinone was MK-8. The DNA G+C contents of strains KA1(T) and WH120(T) were 54.1 and 51.7 mol%, respectively. Strains KA1(T) and WH120(T) displayed 97.8% 16S rRNA gene sequence similarity to each other. The closest recognized relatives were Acidobacterium capsulatum and Telmatobacter bradus (93.4-94.3% 16S rRNA gene sequence similarity). These species differed from strains KA1(T) and WH120(T) by their ability to grow under anoxic conditions, the absence of capsules, presence of cell motility and differing fatty acid composition. Based on these differences, the two new isolates are proposed as representing a novel genus, Acidicapsa gen. nov., and two novel species. Acidicapsa borealis gen. nov., sp. nov. is the type species for the new genus with strain KA1(T) (=DSM 23886(T)=LMG 25897(T)=VKM B-2678(T)) as the type strain. The name Acidicapsa ligni sp. nov. is proposed for strain WH120(T) (=LMG 26244(T)=VKM B-2677(T)=NCCB 100371(T)). PMID:21856984

Kulichevskaya, Irina S; Kostina, Lilia A; Valásková, Vendula; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe; de Boer, Wietse; Dedysh, Svetlana N

2012-07-01

336

Ultrastructure and molecular phylogenetic position of a novel euglenozoan with extrusive episymbiotic bacteria: Bihospites bacati n. gen. et sp. (Symbiontida)  

PubMed Central

Background Poorly understood but highly diverse microbial communities exist within anoxic and oxygen-depleted marine sediments. These communities often harbour single-celled eukaryotes that form symbiotic associations with different prokaryotes. During low tides in South-western British Columbia, Canada, vast areas of marine sand become exposed, forming tidal pools. Oxygen-depleted sediments within these pools are distinctively black at only 2-3 cm depth; these layers contain a rich variety of microorganisms, many of which are undescribed. We discovered and characterized a novel (uncultivated) lineage of heterotrophic euglenozoan within these environments using light microscopy, scanning and transmission electron microscopy, serial sectioning and ultrastructural reconstruction, and molecular phylogenetic analyses of small subunit rDNA sequences. Results Bihospites bacati n. gen. et sp. is a biflagellated microbial eukaryote that lives within low-oxygen intertidal sands and dies within a few hours of exposure to atmospheric oxygen. The cells are enveloped by two different prokaryotic episymbionts: (1) rod-shaped bacteria and (2) longitudinal strings of spherical bacteria, capable of ejecting an internal, tightly wound thread. Ultrastructural data showed that B. bacati possesses all of the euglenozoan synapomorphies. Moreover, phylogenetic analyses of SSU rDNA sequences demonstrated that B. bacati groups strongly with the Symbiontida: a newly established subclade within the Euglenozoa that includes Calkinsia aureus and other unidentified organisms living in low-oxygen sediments. B. bacati also possessed novel features, such as a compact C-shaped rod apparatus encircling the nucleus, a cytostomal funnel and a distinctive cell surface organization reminiscent of the pellicle strips in phagotrophic euglenids. Conclusions We characterized the ultrastructure and molecular phylogenetic position of B. bacati n. gen. et sp. Molecular phylogenetic analyses demonstrated that this species belongs to the Euglenozoa and currently branches as the earliest diverging member of the Symbiontida. This is concordant with ultrastructural features of B. bacati that are intermediate between C. aureus and phagotrophic euglenids, indicating that the most recent ancestor of the Symbiontida descended from phagotrophic euglenids. Additionally, the extrusive episymbionts in B. bacati are strikingly similar to so-called "epixenosomes", prokaryotes previously described in a ciliate species and identified as members of the Verrucomicrobia. These parallel symbioses increase the comparative context for understanding the origin(s) of extrusive organelles in eukaryotes and underscores how little we know about the symbiotic communities of marine benthic environments.

2010-01-01

337

A Network Pharmacology Approach to Determine Active Compounds and Action Mechanisms of Ge-Gen-Qin-Lian Decoction for Treatment of Type 2 Diabetes  

PubMed Central

Traditional Chinese medicine (TCM) herbal formulae can be valuable therapeutic strategies and drug discovery resources. However, the active ingredients and action mechanisms of most TCM formulae remain unclear. Therefore, the identification of potent ingredients and their actions is a major challenge in TCM research. In this study, we used a network pharmacology approach we previously developed to help determine the potential antidiabetic ingredients from the traditional Ge-Gen-Qin-Lian decoction (GGQLD) formula. We predicted the target profiles of all available GGQLD ingredients to infer the active ingredients by clustering the target profile of ingredients with FDA-approved antidiabetic drugs. We also applied network target analysis to evaluate the links between herbal ingredients and pharmacological actions to help explain the action mechanisms of GGQLD. According to the predicted results, we confirmed that a novel antidiabetic ingredient from Puerariae Lobatae radix (Ge-Gen), 4-Hydroxymephenytoin, increased the insulin secretion in RIN-5F cells and improved insulin resistance in 3T3-L1 adipocytes. The network pharmacology strategy used here provided a powerful means for identifying bioactive ingredients and mechanisms of action for TCM herbal formulae, including Ge-Gen-Qin-Lian decoction.

Li, Huiying; Zhao, Linhua; Zhang, Bo; Jiang, Yuyu; Wang, Xu; Guo, Yun; Liu, Hongxing; Li, Shao; Tong, Xiaolin

2014-01-01

338

Enhancing the usability and performance of structured association mapping algorithms using automation, parallelization, and visualization in the GenAMap software system  

PubMed Central

Background Structured association mapping is proving to be a powerful strategy to find genetic polymorphisms associated with disease. However, these algorithms are often distributed as command line implementations that require expertise and effort to customize and put into practice. Because of the difficulty required to use these cutting-edge techniques, geneticists often revert to simpler, less powerful methods. Results To make structured association mapping more accessible to geneticists, we have developed an automatic processing system called Auto-SAM. Auto-SAM enables geneticists to run structured association mapping algorithms automatically, using parallelization. Auto-SAM includes algorithms to discover gene-networks and find population structure. Auto-SAM can also run popular association mapping algorithms, in addition to five structured association mapping algorithms. Conclusions Auto-SAM is available through GenAMap, a front-end desktop visualization tool. GenAMap and Auto-SAM are implemented in JAVA; binaries for GenAMap can be downloaded from http://sailing.cs.cmu.edu/genamap.

2012-01-01

339

Sensitivity evaluation of the Gen-Probe AMP-CT assay by pooling urine samples for the screening of Chlamydia trachomatis urogenital infection.  

PubMed

The sensitivity of two urine pool sizes versus individual testing, to detect Chlamydia trachomatis urogenital infection, was evaluated using the Gen-Probe AMP-CT assay. Thirty-three (33) known polymerase chain reaction (PCR) positive urine specimens were combined with 231 fresh first-catch urine (FCU) samples in 33 groups of four and 33 groups of eight, to make up 4X and 8X pooled samples, respectively. Gen-Probe AMP-CT assay was performed on pools as well as on individual samples at the same time. For the discrepant cases, the known positive samples were diluted 1:4 and 1:8 using the manufacturer's dilution buffer and were retested. Additional positive specimens found among fresh FCU samples were also tested by the Amplicor-PCR assay to confirm their positivity. The sensitivities of 8X pooling, 4X pooling and individual testing were 86.5%, 94.3% and 91.9%, respectively. The Gen-Probe AMP-CT assay applied to a 4X urine pooling model was highly sensitive and may be useful for a population based screening programme. PMID:12194735

Gomes, J P; Viegas, S; Paulino, A; Catry, M A

2002-08-01

340

The Columbus Knee System: 4-Year Results of a New Deep Flexion Design Compared to the NexGen Full Flex Implant  

PubMed Central

The Columbus knee system is designed as a standard knee implant to allow high flexion without additional bone resection. Between August, 2004 and March, 2010 we performed 109 total knee arthroplasties of the Columbus knee system in 101 consecutive patients suffering from primary arthrosis of the knee. Mean age was 72.4 years in women and 70.3 years in men. Mean followup was 47.3 months. The 4-year results of a group of patients who received the NexGen Full Flex implant operated by the same surgeon were used for comparison. Mean total knee score was Columbus: 175.6 and NexGen Flex: 183.4; P = 0.037. Mean operation time was 53?min for Columbus and 66?min for NexGen Flex; P < 0.001. With new streamlined instruments operative time became 60?min for the Columbus; P > 0.05. Radiological assessment showed no signs of loosening for both groups. Therefore, the Columbus knee system can be recommended for flexion angles up to 140°.

Goebel, D.; Schultz, W.

2012-01-01

341

Gen-Struktur und Gen-Expression  

NASA Astrophysics Data System (ADS)

In the chicken oviduct the synthesis of the egg-white proteins ovalbumin, conalbumin, ovomucoid and lysozyme is controlled by the female sex steroids. The steroid-controlled rate of synthesis of these proteins is closely correlated to the cellular concentration of the egg-white protein mRNAs. The accumulation of these mRNAs is achieved by a drecreased rate of degradation and an increased rate of synthesis. To understand the molecular mechanism that regulates the expression of this group of genes we have isolated the lysozyme and ovomucoid gene by gene-cloning. The structure and expression of the lysozyme gene has been studied.

Schütz, Günther

1981-04-01

342

Isolation and characterization of Keratinibaculum paraultunense gen. nov., sp. nov., a novel thermophilic, anaerobic bacterium with keratinolytic activity.  

PubMed

A novel thermophilic, anaerobic, keratinolytic bacterium designated KD-1 was isolated from grassy marshland. Strain KD-1 was a spore-forming rod with a Gram-positive type cell wall, but stained Gram-negative. The temperature, pH, and NaCl concentration range necessary for growth was 30-65 °C (optimum 55 °C), 6.0-10.5 (optimum 8.0-8.5), and 0-6% (optimum 0.2%) (w/v), respectively. Strain KD-1 possessed extracellular keratinase, and the optimum activity of the crude enzyme was pH 8.5 and 70 °C. The enzyme was identified as a thermostable serine-type protease. The strain was sensitive to rifampin, chloramphenicol, kanamycin, and tetracycline and was resistant to erythromycin, neomycin, penicillin, and streptomycin. The main cellular fatty acid was predominantly C15:0 iso (64%), and the G+C content was 28 mol%. Morphological and physiological characterization, together with phylogenetic analysis based on 16S rRNA gene sequencing identified KD-1 as a new species of a novel genus of Clostridiaceae with 95.3%, 93.8% 16S rRNA gene sequence similarity to Clostridium ultunense BS(T) (DSM 10521(T)) and Tepidimicrobium xylanilyticum PML14(T) (= JCM 15035(T)), respectively. We propose the name Keratinibaculum paraultunense gen. nov., sp. nov., with KD-1 (=JCM 18769(T) =DSM 26752(T)) as the type strain. PMID:23710623

Huang, Yan; Sun, Yingjie; Ma, Shichun; Chen, Lu; Zhang, Hui; Deng, Yu

2013-08-01

343

Robinsoniella peoriensis gen. nov., sp. nov., isolated from a swine-manure storage pit and a human clinical source.  

PubMed

A polyphasic taxonomic study was performed on six strains of an unknown Gram-positive, non-motile, spore-forming, short oval to rod-shaped bacterium isolated from a swine-manure storage pit. In addition to these strains, an isolate deposited in the Culture Collection of the University of Göteborg (Sweden) was found to be biochemically related to the manure strains. The major end products of metabolism included acetate and succinate but not butyrate. Comparative 16S rRNA gene sequencing confirmed that all these isolates were closely related to each other and formed a hitherto unknown lineage within the clostridial rRNA XIVa cluster of organisms. On the basis of phylogenetic, biochemical and phenotypic evidence, it is proposed that the unknown bacterium represents a novel genus and species, for which the name Robinsoniella peoriensis gen. nov., sp. nov. is proposed. The type strain of Robinsoniella peoriensis is PPC31T (=CCUG 48729T =NRRL B-23985T). PMID:19126740

Cotta, Michael A; Whitehead, Terence R; Falsen, Enevold; Moore, Edward; Lawson, Paul A

2009-01-01

344

The Ultramicrobacterium "Elusimicrobium minutum" gen. nov., sp. nov., the First Cultivated Representative of the Termite Group 1 Phylum? †  

PubMed Central

Insect intestinal tracts harbor several novel, deep-rooting clades of as-yet-uncultivated bacteria whose biology is typically completely unknown. Here, we report the isolation of the first representative of the termite group 1 (TG1) phylum from sterile-filtered gut homogenates of a humivorous scarab beetle larva. Strain Pei191T is a mesophilic, obligately anaerobic ultramicrobacterium with a gram-negative cell envelope. Cells are typically rod shaped, but cultures are pleomorphic in all growth phases (0.3 to 2.5 ?m long and 0.17 to 0.3 ?m wide). The isolate grows heterotrophically on sugars and ferments d-galactose, d-glucose, d-fructose, d-glucosamine, and N-acetyl-d-glucosamine to acetate, ethanol, hydrogen, and alanine as major products but only if amino acids are present in the medium. PCR-based screening and comparative 16S rRNA gene sequence analysis revealed that strain Pei191T belongs to the “intestinal cluster,” a lineage of hitherto uncultivated bacteria present in arthropod and mammalian gut systems. It is only distantly related to the previously described so-called “endomicrobia” lineage, which comprises mainly uncultivated endosymbionts of termite gut flagellates. We propose the name “Elusimicrobium minutum” gen. nov., sp. nov. (type strain, Pei191T = ATCC BAA-1559T = JCM 14958T) for the first isolate of this deep-branching lineage and the name “Elusimicrobia” phyl. nov. for the former TG1 phylum.

Geissinger, Oliver; Herlemann, Daniel P. R.; Morschel, Erhard; Maier, Uwe G.; Brune, Andreas

2009-01-01

345

Description of Fimbriimonas ginsengisoli gen. nov., sp. nov. within the Fimbriimonadia class nov., of the phylum Armatimonadetes.  

PubMed

Strain Gsoil 348(T) was isolated from a ginseng field soil sample by selecting micro-colonies from one-fifth strength modified R2A agar medium after a long incubation period. 16S rRNA gene sequence analysis indicated that the strain is related to members of the phylum Armatimonadetes (formerly called candidate phylum OP10). Strain Gsoil 348(T) is mesophilic, strictly aerobic, non-motile and rod-shaped. It only grows in low nutrient media. The major respiratory quinones are menaquinones MK-11 and MK-10, and the main fatty acids are iso-C(15:0), iso-C(17:0), C(16:0) and C(16:1) ?11c. The G+C content is 61.4 mol%. The 16S rRNA gene sequences in public databases belonging to the phylum Armatimonadetes were clustered here into 6 groups. Five of these groups constituted a coherent cluster distinct from the sequences of other phyla in phylogenetic trees that were constructed using multiple-outgroup sequences from 49 different phyla. On the basis of polyphasic taxonomic analyses, it is proposed that strain Gsoil 348(T) (= KACC 14959(T) = JCM 17079(T)) should be placed in Fimbriimonas ginsengisoli gen. nov., sp. nov., as the cultured representative of the Fimbriimonadia class. nov., corresponding with Group 4 of the phylum Armatimonadetes. PMID:22527625

Im, Wan-Taek; Hu, Zi-Ye; Kim, Kyoung-Ho; Rhee, Sung-Keun; Meng, Han; Lee, Sung-Taik; Quan, Zhe-Xue

2012-08-01

346

Phylogenetic analysis identifies the 'megabacterium' of birds as a novel anamorphic ascomycetous yeast, Macrorhabdus ornithogaster gen. nov., sp. nov.  

PubMed

An organism commonly referred to as 'megabacterium' colonizes the gastric isthmus of many species of birds. It is weakly gram-positive and periodic acid-Schiff-positive and stains with silver stains. Previous studies have shown that it has a nucleus and a cell wall similar to those seen in fungi. Calcofluor white M2R staining suggests that the cell wall contains chitin, a eukaryote-specific substance, and rRNA in situ hybridization demonstrates that it is a eukaryote. To characterize this organism phylogenetically, DNA was extracted from purified cells. rDNA was readily amplified by PCR with pan-fungal DNA primer sets and primer sets derived from the newly determined sequence, but not with bacteria-specific primer sets. Specific primer sets amplified rDNA from isthmus scrapings from an infected bird, but not from a non-infected bird or other control DNA. The sequence was confirmed to derive from the purified organism by in situ rRNA hybridization using a specific probe. Phylogenetic analysis of sequences of the 18S rDNA and domain D1/D2 of 26S rDNA showed the organism to be a previously undescribed anamorphic ascomycetous yeast representing a new genus. The name Macrorhabdus ornithogaster gen. nov., sp. nov. is proposed for this organism. The type material is CBS 9251T (= NRRL Y-27487T). PMID:12892150

Tomaszewski, Elizabeth K; Logan, Kathleen S; Snowden, Karen F; Kurtzman, Cletus P; Phalen, David N

2003-07-01

347

Mameliella alba gen. nov., sp. nov., a marine bacterium of the Roseobacter clade in the order Rhodobacterales.  

PubMed

A Gram-negative, non-motile, rod-shaped bacterial strain, JLT354-W(T), that accumulates poly-beta-hydroxybutyrate granules was isolated from the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was related to members of the genera Antarctobacter, Sagittula, Oceanicola and Loktanella; levels of similarity between strain JLT354-W(T) and members of the above genera were less than 92.0 %. The predominant fatty acid of strain JLT354-W(T) was C(18 : 1)omega7c (83.1 %); significant amounts of C(18 : 0) (7.9 %) and C(12 : 1) 3-OH (3.7 %) were also present. The predominant respiratory ubiquinone was Q-10. The DNA G+C content of strain JLT354-W(T) was 63.7 mol%. The isolate was distinguishable from members of the order Rhodobacterales based on phenotypic and biochemical characteristics. On the basis of the taxonomic data presented, strain JLT354-W(T) is considered to represent a novel species of a new genus, for which the name Mameliella alba gen. nov., sp. nov. is proposed. The type strain of Mameliella alba is JLT354-W(T) (=LMG 24665(T)=CGMCC 1.7290(T)). PMID:19661508

Zheng, Qiang; Chen, Chuang; Yan, Xiao-Jun; Wang, Ya-Nan; Zeng, Yong-Hui; Hao, Li-Kai; He, Wei-Hong; Jiao, Nian-Zhi

2010-04-01

348

Haloalkaliphilic spore-forming sulfidogens from soda lake sediments and description of Desulfitispora alkaliphila gen. nov., sp. nov.  

PubMed Central

An anaerobic enrichment with pyruvate as electron donor and thiosulfate at pH 10 and 0.6 M Na+ inoculated with pasteurized soda lake sediments resulted in a sulfidogenic coculture of two morphotypes of obligately anaerobic haloalkaliphilic endospore-forming clostridia, which were further isolated in pure culture. Strain AHT16 was a thin long rod able to ferment sugars and pyruvate and to respire H2, formate and pyruvate using thiosulfate and fumarate as electron acceptors and growing optimally at pH 9.5. Thiosulfate was reduced incompletely to sulfide and sulfite. The strain was closely related (99% sequence similarity) to a peptolytic alkaliphilic clostridium Natronincola peptidovorans. Strain AHT17 was a short rod with a restricted respiratory metabolism, growing with pyruvate and lactate as electron donor and sulfite, thiosulfate and elemental sulfur as electron acceptors with a pH optimum 9.5. Thiosulfate was reduced completely via sulfite to sulfide. The ability of AHT17 to use sulfite explained the stability of the original coculture of the two clostridia—one member forming sulfite from thiosulfate and another consuming it. Strain AHT17 formed an independent deep phylogenetic lineage within the Clostridiales and is proposed as a new genus and species Desulfitisporum alkaliphilum gen. nov., sp. nov. (=DSM 22410T = UNIQEM U794T). Electronic supplementary material The online version of this article (doi:10.1007/s00792-010-0310-y) contains supplementary material, which is available to authorized users.

Muyzer, Gerard

2010-01-01

349

The eGenVar data management system--cataloguing and sharing sensitive data and metadata for the life sciences  

PubMed Central

Systematic data management and controlled data sharing aim at increasing reproducibility, reducing redundancy in work, and providing a way to efficiently locate complementing or contradicting information. One method of achieving this is collecting data in a central repository or in a location that is part of a federated system and providing interfaces to the data. However, certain data, such as data from biobanks or clinical studies, may, for legal and privacy reasons, often not be stored in public repositories. Instead, we describe a metadata cataloguing system and a software suite for reporting the presence of data from the life sciences domain. The system stores three types of metadata: file information, file provenance and data lineage, and content descriptions. Our software suite includes both graphical and command line interfaces that allow users to report and tag files with these different metadata types. Importantly, the files remain in their original locations with their existing access-control mechanisms in place, while our system provides descriptions of their contents and relationships. Our system and software suite thereby provide a common framework for cataloguing and sharing both public and private data. Database URL: http://bigr.medisin.ntnu.no/data/eGenVar/

Razick, Sabry; Mocnik, Rok; Thomas, Laurent F.; Ryeng, Einar; Drabl?s, Finn; Saetrom, Pal

2014-01-01

350

Conexibacter woesei gen. nov., sp. nov., a novel representative of a deep evolutionary line of descent within the class Actinobacteria.  

PubMed

A novel Gram-positive bacterial strain was isolated from forest soil. According to its 16S rRNA sequence, this strain is a deep-rooting member of the class Actinobacteria. The 16S rRNA sequence is most closely related (approximately 94% identity) to clones of uncultured bacteria detected in different terrestrial environments, while showing only a remote relationship (approximately 90% identity or less) to sequences of cultured species. Cells of the first cultured representative of this phylogenetic cluster are small, short rods that are motile by peritrichous flagella, catalase- and oxidase-positive and grow under aerobic conditions. In liquid culture, flagella from different cells can aggregate to form networks, clearly visible under the light microscope. The peptidoglycan contains meso-diaminopimelic acid and is directly cross-linked (type A1gamma). Mycolic acids are not present. The polar lipids are phosphatidylinositol and an unidentified phospholipid. Menaquinone MK-7(H4) was detected as the predominant isoprenoid quinone. Oleic, 14-methylpentadecanoic, hexadecanoic and omega6c-heptadecenoic acids are the predominant components of the cellular fatty acid profile. The DNA G + C content is 71 mol%. The distinct phylogenetic position and the unusual combination of chemotaxonomic characteristics justify the proposal of a new genus and species, Conexibacter woesei gen. nov., sp. nov., with the type strain ID131577T (=DSM 14684T =JCM 11494T). PMID:12710628

Monciardini, Paolo; Cavaletti, Linda; Schumann, Peter; Rohde, Manfred; Donadio, Stefano

2003-03-01

351

Silanimonas lenta gen. nov., sp. nov., a slightly thermophilic and alkaliphilic gammaproteobacterium isolated from a hot spring.  

PubMed

A moderately thermophilic aerobic bacterium, strain 25-4T, was isolated from a hot spring at Baekdoo Mountain in Korea. The cells were Gram-negative, motile rods each having a polar flagellum. Analysis of the 16S rRNA gene sequence indicated that the strain represented a new lineage within the family 'Xanthomonadaceae' of the 'Gammaproteobacteria', being most closely related to the genera Thermomonas, Xanthomonas, Luteimonas, Pseudoxanthomonas, Stenotrophomonas and Xylella and having 16S rRNA gene sequence similarities to the most related species of the genera of between 92.9 and 94.4 %. The strain contained Q-8 as the major isoprenoid quinone and had a fatty acid profile with predominant iso-branched fatty acids. Growth occurred at pH 6.0-10, with an optimum at pH 9.0, and at 25-53 degrees C, with an optimum at 47 degrees C. The G+C content of the genomic DNA was 50.7 mol%. On the basis of phylogenetic analyses and its phenotypic characteristics, strain 25-4T belongs to a new genus, Silanimonas gen. nov., within the 'Gammaproteobacteria'. The sole species of this genus is Silanimonas lenta sp. nov. (type strain, 25-4T=DSM 16282T=KCTC 12236T). PMID:15653905

Lee, Eun Mi; Jeon, Che Ok; Choi, Inpyo; Chang, Kyu-Seob; Kim, Chang-Jin

2005-01-01

352

Morphology and ontogenesis of Psilotrichides hawaiiensis nov. gen., nov. spec. and molecular phylogeny of the Psilotrichidae (Ciliophora, Hypotrichia).  

PubMed

The Psilotrichidae are a family of middle-sized hypotrichs with unique morphological and ontogenetic features (e.g. the oral primordium develops in a deep pouch) that, however, did not provide a definite phylogenetic signal. Thus, we studied the 18S rRNA gene of Urospinula succisa (Müller 1786) Esteban et al., 2001 as well as the morphology and ontogenesis of Psilotrichides hawaiiensis, a new genus and species from an ephemeral swamp on Oahu Island, Hawaii. The molecular data classify the psilotrichids into the oxytrichids but without clear branching position. A brief revision, using the structure of the oral apparatus, the location of the contractile vacuole, and three ontogenetic features, showed four distinct genera: Psilotricha Stein, 1859; Urospinula Corliss, 1960; Hemiholosticha Gelei, 1954; and Psilotrichides nov. gen., which differs from the confamilials mainly by the obliquely oriented buccal cavity and the shape of the undulating membranes as well as by a distinct ridge along the right buccal margin. The pyriform species, P. hawaiiensis, is about 65 × 45 ?m in size and is easily recognized by the table tennis racket-shaped appearance due to the elongated last cirrus of the left marginal row. Refined diagnoses are provided for the family Psilotrichidae Bütschli, 1889 and the genera contained. PMID:24498929

Heber, Domingo; Stoeck, Thorsten; Foissner, Wilhelm

2014-01-01

353

Rigifila ramosa n. gen., n. sp., a filose apusozoan with a distinctive pellicle, is related to Micronuclearia.  

PubMed

We report the ultrastructure, 18S and 28S rDNA sequences, and phylogenetic position of a distinctive free-living heterotrophic filose protist, Rigifila ramosa n. gen., n. sp., from a freshwater paddyfield. Rigifila lacks cilia and has a semi-rigid, radially symmetric, well-rounded, partially microtubule-supported, dorsal pellicle, and flat mitochodrial cristae. From a central aperture in a ventral depression emerges a protoplasmic stem that branches into several branching filopodia that draw bacteria to it. Electron microscopy reveals a general cell structure similar to Micronuclearia, the only non-flagellate previously known in Apusozoa; the large basal vacuole is probably an unusual giant contractile vacuole. Phylogenetic analysis of concatenated rDNA sequences groups Rigifila and Micronuclearia as sisters with maximal statistical support. However, novel morphological differences unique to Rigifila, notably a double (not single) proteinaceous layer beneath the cell membrane, and cortical microtubules, lead us to place it in a new family Rigifilidae. Our morphological and molecular analyses show that Rigifila is the closest known relative of Micronuclearia. Therefore we group Micronucleariidae and Rigifilidae as a new order Rigifilida within the existing class Hilomonadea, which now excludes planomonads. Rigifilida groups weakly with Collodictyon (Diphyllatea). We discuss the possible relationships of Rigifilida to other Apusozoa and Diphyllatea. PMID:22682062

Yabuki, Akinori; Ishida, Ken-Ichiro; Cavalier-Smith, Thomas

2013-01-01

354

Salarchaeum japonicum gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea isolated from commercial salt.  

PubMed

Strain YSM-79(T) was isolated from commercial salt made from seawater in Yonaguni island, Okinawa, Japan. The strain is an aerobic, Gram-negative, chemo-organotrophic and extremely halophilic archaeon. Cells are short rods that lyse in distilled water. Growth occurs at 1.5-5.3 M NaCl (optimum 2.5-3.0 M), pH 5.0-8.8 (optimum pH 5.2-6.3) and 20-55 °C (optimum 40 °C). Mg²? is required for growth, with maximum growth at 200-300 mM Mg²?. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylglycerophosphate methyl ester, sulfated diglycosyl diether-1 and five unidentified glycolipids. The G+C content of the DNA was 64 mol%. On the basis of 16S rRNA gene sequence analysis, strain YSM-79(T) was determined to be a member of the family Halobacteriaceae, with the closest related genus being Halobacterium (94?% sequence identity). In addition, the rpoB' gene sequence of strain YSM-79(T) had <88?% sequence similarity to those of other members of the family Halobacteriaceae. The results of phenotypic, chemotaxonomic and phylogenetic analysis suggested that strain YSM-79(T) should be placed in a new genus, Salarchaeum gen. nov., as a representative of Salarchaeum japonicum sp. nov. The type strain is YSM-79(T) (?=?JCM 16327(T) ?=?CECT 7563(T)). PMID:20952548

Shimane, Yasuhiro; Hatada, Yuji; Minegishi, Hiroaki; Echigo, Akinobu; Nagaoka, Syuhei; Miyazaki, Masayuki; Ohta, Yukari; Maruyama, Tadashi; Usami, Ron; Grant, William D; Horikoshi, Koki

2011-09-01

355

Cloacibacterium normanense gen. nov., sp. nov., a novel bacterium in the family Flavobacteriaceae isolated from municipal wastewater.  

PubMed

Phenotypic and phylogenetic studies were performed on three isolates of an unknown Gram-negative, facultatively anaerobic, non-motile, yellow-pigmented, rod-shaped organism isolated from raw sewage. 16S rRNA gene sequence analysis indicated that these strains were members of the Bergeyella-Chryseobacterium-Riemerella branch of the family Flavobacteriaceae. The unknown bacterium was readily distinguished from reference strains by 16S rRNA gene sequencing and biochemical tests. The organism contained menaquinone MK-6 as the predominant respiratory quinone and had a DNA G+C content of 31 mol%. A most probable number-PCR approach was developed to detect, and estimate the numbers of, this organism. Untreated wastewater from one plant yielded an estimated count of 1.4 x 10(5) cells ml(-1), and untreated wastewater from a second plant yielded an estimated count of 1.4 x 10(4) cells ml(-1). Signal was not detected from treated effluent or from human stool specimens. On the basis of the results of the study presented, it is proposed that the unknown bacterium be classified in a novel genus Cloacibacterium, as Cloacibacterium normanense gen. nov., sp. nov., which is also the type species. The type strain of Cloacibacterium normanense is strain NRS1(T) (=CCUG 46293(T) = CIP 108613(T) = ATCC BAA-825(T) = DSM 15886(T)). PMID:16738108

Allen, Toby D; Lawson, Paul A; Collins, Matthew D; Falsen, Enevold; Tanner, Ralph S

2006-06-01

356

Microbotryozyma collariae gen. nov., sp. nov., a basidiomycetous yeast isolated from a plant bug Collaria oleosa (Miridae).  

PubMed

Two strains of a basidiomycetous yeast were derived from an insect trypanosomatid culture isolated from the intestine of a plant bug, Collaria oleosa (Heteroptera: Miridae), collected in Costa Rica. The yeast did not form ballistoconidia but reproduced only by budding. Teliospores were not observed in individual and crossed cultures of each strain. Morphological and other taxonomic characteristics of the yeast were similar to those of the species in the polyphyletic genus Rhodotorula. However, molecular phylogeny inferred from the internal transcribed spacers and D1/D2 region of the large subunit rRNA gene showed that the strains represent a new species placed among the smut fungi in the family Ustilentylomataceae, which includes Aurantiosporium subnitens, Fulvisporium restifaciens, Ustilentyloma fluitans, and Rhodotorula hordea. Given the well distinguished phylogenetic position of this novel species within the Ustilentylomataceae, we propose Microbotryozyma collariae gen. nov., sp. nov. to accommodate the yeast isolated from C. oleosa, with strain American Type Culture Collection MYA-4666(T) (= PRA303-1S = CBS 12537) designated as the type strain. PMID:22407501

Suh, Sung-Oui; Maslov, Dmitri A; Molestina, Robert E; Zhou, Jianlong J

2012-06-01

357

Results From a Parametric Acoustic Liner Experiment Using P and W GEN1 HSR Mixer/Ejector Model  

NASA Technical Reports Server (NTRS)

This report documents the results of an acoustic liner test performed using a Gen 1 HSR mixer/ejector model installed on the Jet Exit Rig in the Nozzle Acoustic Test Rig in the Aeroacoustic Propulsion Laboratory or NASA Glenn Research Center. Acoustic liner effectiveness and single-component thrust performance results are discussed. Results from 26 different types of single-degree-of-freedom and bulk material liners are compared with each other and against a hardwall baseline. Design parameters involving all aspects of the facesheet, the backing cavity, and the type of bulk material were varied in order to study the effects of these design features on the acoustic impedance, acoustic effectiveness and on nozzle thrust performance. Overall, the bulk absorber liners are more effective at reducing the jet noise than the single-degree-of-freedom liners. Many of the design parameters had little effect on acoustic effectiveness, such as facesheeet hole diameter and honeycomb cell size. A relatively large variation in the impedance of the bulk absorber in a bulk liner is required to have a significant impact on the noise reduction. The thrust results exhibit a number of consistent trends, supporting the validity of this new addition to the facility. In general, the thrust results indicate that thrust performance benefits from increased facesheet thickness and decreased facesheet porosity.

Boyd, Kathleen C.; Wolter, John D.

2004-01-01

358

Sediminibacterium salmoneum gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment of a eutrophic reservoir.  

PubMed

Strain NJ-44(T), isolated from sediment of the eutrophic Guanting Reservoir in Beijing (China), was subjected to a taxonomic study using a polyphasic approach. The strain was aerobic, with salmon-pink-pigmented colonies on R2A agar. Cells were single, Gram-negative rods, motile by gliding. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain NJ-44(T) belonged to the phylum Bacteroidetes, with Terrimonas ferruginea ATCC 13524(T) (90.8% similarity), Terrimonas lutea DY(T) (90.5%) and Niabella aurantiaca R2A15-11(T) (89.1%) as its closest relatives. Strain NJ-44(T) was clearly differentiated from members of the genera Terrimonas and Niabella in its DNA G+C content (40.6 mol%) and its major fatty acids, iso-C(15:1) G, iso-C(15:0), anteiso-C(15:0), iso-C(16:0) 3-OH, iso-C(17:0) 3-OH, anteiso-C(15:1) A and iso-C(15:0) 3-OH. It is proposed that strain NJ-44(T) represents a novel genus and species, named Sediminibacterium salmoneum gen. nov., sp. nov. The type strain of Sediminibacterium salmoneum is strain NJ-44(T) (=CGMCC 1.6845(T) =NBRC 103935(T)). PMID:18768628

Qu, Jian-Hang; Yuan, Hong-Li

2008-09-01

359

Coenonia anatina gen. nov., sp. nov., a novel bacterium associated with respiratory disease in ducks and geese.  

PubMed

Taxon 1502 was originally described as a Riemerella anatipestifer-like bacterium causing exudative septicaemia in ducks and geese. In the present study, an integrated genotypic and phenotypic approach was used to elucidate the phylogenetic affiliation and taxonomic relationships of 12 strains of taxon 1502. Whole-cell protein and fatty acid analyses and an extensive biochemical examination by using conventional tests and several API microtest systems indicated that all isolates formed a homogeneous taxon, which was confirmed by DNA-DNA hybridizations. 16S rDNA sequence analysis of a representative strain (LMG 14382T) indicated that this taxon belongs to the Cytophaga-Flavobacterium-Bacteroides phylum and revealed a moderate but distinct relationship to species of the genus Capnocytophaga (overall 16S rDNA sequence identities were 88.8-90.2%). Taxon 1502 is concluded to represent a single species that should be allocated to a novel genus, and the name Coenonia anatina gen. nov., sp. nov. is proposed. The DNA G + C content of representative strains was 35-36 mol% and the type strain is LMG 14382T. PMID:10319512

Vandamme, P; Vancanneyt, M; Segers, P; Ryll, M; Köhler, B; Ludwig, W; Hinz, K H

1999-04-01

360

Schmidingerothrix extraordinaria nov. gen., nov. spec., a secondarily oligomerized hypotrich (Ciliophora, Hypotricha, Schmidingerotrichidae nov. fam.) from hypersaline soils of Africa  

PubMed Central

Schmidingerothrix extraordinaria nov. gen., nov. spec. was discovered in hypersaline soils from Namibia and Egypt. Its morphology and ontogenesis were studied with standard methods. Schmidingerothrix extraordinaria is a highly flexible, slender hypotrich with an average size of 90 × 15 ?m. Likely, it prefers a salinity around 100‰ and feeds mainly on bacteria. Schmidingerothrix is extraordinary in having a frayed buccal lip, three-rowed adoral membranelles, only one frontal cirrus, a distinct gap between frontal and ventral adoral membranelles, and a miniaturized first frontal membranelle, while a paroral membrane, dorsal bristle rows, and buccal, transverse, and caudal cirri are absent. The ontogenesis is simple: the opisthe oral apparatus and frontoventral ciliature originate de novo, while parental structures are involved in the development of the ciliature of the proter. This special organization is used to define a new family, the Schmidingerotrichidae, which is likely related to the Cladotrichidae. Schmidingerothrix extraordinaria is very likely a secondarily oligomerized hypotrich, and the reduction occurred possibly very long ago because no traces of the ancestral ciliature remained in the ontogenetic processes. Possibly, the simple ciliature is an adaptation to highly saline habitats, where competition is low and bacterial food abundant.

Foissner, Wilhelm

2012-01-01

361

Tanticharoenia sakaeratensis gen. nov., sp. nov., a new osmotolerant acetic acid bacterium in the alpha-Proteobacteria.  

PubMed

Tanticharoenia sakaeratensis gen. nov., sp. nov. is proposed for three strains isolated from soil collected in Thailand. The three strains, AC37(T), AC38, and AC39, were included within a lineage comprising the genera Asaia, Kozakia, Swaminathania, Neoasaia, Acetobacter, Gluconobacter, and Saccharibacter in a phylogenetic tree based on 16S rRNA gene sequences, but formed a quite different, independent cluster. Pair-wise sequence similarities of strain AC37(T) were 96.5-92.1% to the type strains of Acetobacter aceti, Gluconobacter oxydans, Acidomonas methanolica, Gluconacetobacter liquefaciens, Asaia bogorensis, Kozakia baliensis, Swaminathania salitolerans, Saccharibacter floricola, Neoasaia chiangmaiensis, and Granulibacter bethesdensis. The three strains had DNA base compositions comprising respectively 65.6, 64.5, and 65.6 mol % G+C with a range of 1.1 mol %, and formed a single species. Phenotypically, the three strains did not oxidize acetate or lactate, but grew on 30% D-glucose (w/v). Chemotaxonomically, they had Q-10. The type strain is AC37(T) (= BCC 15772(T) = NBRC 103193(T)). PMID:18323667

Yukphan, Pattaraporn; Malimas, Taweesak; Muramatsu, Yuki; Takahashi, Mai; Kaneyasu, Mika; Tanasupawat, Somboon; Nakagawa, Yasuyoshi; Suzuki, Ken-ichiro; Potacharoen, Wanchern; Yamada, Yuzo

2008-03-01

362

Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine.  

PubMed

A novel extreme alkaliphile was isolated from a mine water containment dam at 3.2 km below land surface in an ultra-deep gold mine near Carletonville, South Africa. The cells of this bacterium were straight to slightly curved rods, motile by flagella and formed endospores. Growth was observed over the temperature range 20-50 degrees C (optimum 40 degrees C; 45 min doubling time) and pH range 8.5-12.5 (optimum pH 10.0). The novel isolate, one of the most alkaliphilic micro-organisms yet described, was a strictly anaerobic chemo-organotroph capable of utilizing proteinaceous substrates such as yeast extract, peptone, tryptone and casein. Elemental sulfur, thiosulfate or fumarate, when included as accessory electron acceptors, improved growth. The G+C content of genomic DNA was 36.4 mol %. Phylogenetic analysis based on the 16S rDNA sequence indicated that the isolate is a member of cluster XI within the low G+C gram-positive bacteria, but only distantly related to previously described members. On the basis of physiological and molecular properties, the isolate represents a novel species, for which the name Alkaliphilus transvaalensis gen. nov., sp. nov. is proposed (type strain SAGM1T = JCM 10712T = ATCC 700919T). The mechanism of generation of the highly alkaline microbial habitat and the possible source of the alkaliphile are discussed. PMID:11491320

Takai, K; Moser, D P; Onstott, T C; Spoelstra, N; Pfiffner, S M; Dohnalkova, A; Fredrickson, J K

2001-07-01

363

New SSU-rDNA sequences for eleven colpodeans (Ciliophora, Colpodea) and description of Apocyrtolophosis nov. gen.  

PubMed

Using 11 new SSU-rDNA sequences, we analyze relationships within the class Colpodea, especially of some uncommon taxa, such as Kalometopia duplicata, Cyrtolophosis minor, and Jaroschia sumptuosa. The sequences do not change the basic structure of the molecular Colpodea tree, i.e., all belong to one of the four molecular clades recognized by Foissner et al. (2011): Colpodida, Cyrtolophosidida, Bursariomorphida, and Platyophryida. The addition of three Colpoda sequences strengthens the observation that species of this genus are distributed over the whole molecular Colpodea tree. Very likely, this is caused by a fast radiation of Colpoda, several species of which then evolved independently, forming new genera and families. Cyrtolophosis minor, which belongs to the molecular Pseudocyrtolophosis clade, is referred to a new genus, Apocyrtolophosis nov. gen., characterized by a comparably large, deltoid oral opening, an unciliated posterior region, and the absence of an oblique kinety in the left oral polykinetid. Bryometopus triquetrus does not erase the paraphyly of its genus. Platyophrya vorax, P. spumacola, and P. bromelicola form a highly supported clade in the order Platyophryida. Platyophryides and Ottowphrya are close genetically but differ in the silverline pattern (colpodid vs. platyophryid). PMID:24210999

Foissner, Wilhelm; Bourland, William A; Wolf, Klaus W; Stoeck, Thorsten; Dunthorn, Micah

2014-02-01

364

Pacificamonas flava gen. nov., sp. nov., a Novel Member of the Family Sphingomonadaceae Isolated from the Southeastern Pacific.  

PubMed

Strain JLT2015(T) was isolated from surface seawater of the Southeastern Pacific. The strain was Gram-negative, aerobic, motile by gliding, and rod shaped. The dominant fatty acids were C18:1?7c, C16:0, and C16:1?7c. The major respiratory ubiquinone was Q-10, and the predominant polyamine pattern was spermidine. The components of the polar lipid profile were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and sphingoglycolipid. The DNA G+C content was 64.2 %. Phylogenetic analysis based on 16S rRNA gene sequence revealed strain JLT2015(T) belonged to belong to the family Sphingomonadaceae, exhibiting 94.7 % 16S rRNA gene sequence similarity with Novosphingobium pentaromativorans. On the basis of the taxonomic data presented, together with phylogenetic and genetic characteristics, strain JLT2015(T) is considered to represent a novel genus, for which the name Pacificamonas flava gen. nov., sp. nov. is proposed. The type strain of Pacificamonas flava is JLT2015(T) (=LMG27364(T) = CGMCC1.12401(T)). PMID:24633861

Liu, Keshao; Li, Shuhui; Jiao, Nianzhi; Tang, Kai

2014-07-01

365

Aquipuribacter hungaricus gen. nov., sp. nov., an actinobacterium isolated from the ultrapure water system of a power plant.  

PubMed

A Gram-positive actinobacterium, strain IV-75(T), was isolated by using R2A agar from the ultrapure water system of a power plant in Hungary. The strain exhibited a rod-coccus cell cycle, and was strictly aerobic, non-motile, catalase-positive and oxidase-negative. 16S rRNA gene sequence analysis revealed that strain IV-75(T) belonged to the suborder Micrococcineae and clustered with members of the family Intrasporangiaceae. Its closest phylogenetic neighbour was Arsenicicoccus bolidensis CCUG 47306(T) (94.3% 16S rRNA gene sequence similarity). The peptidoglycan of strain IV-75(T) contained meso-diaminopimelic acid and MK-10(H(4)) was the major menaquinone. The polar lipid pattern contained phosphatidylglycerol, two unidentified phospholipids, one glycolipid and several other lipid components. The major fatty acids were anteiso-C(15:0), C(18:1)?9c and C(16:0). Based on the moderate levels of 16S rRNA gene sequence similarity to all members of the family Intrasporangiaceae and the unique combination of chemotaxonomic characteristics, strain IV-75(T) is considered to represent a novel species of a new genus, for which the name Aquipuribacter hungaricus gen. nov., sp. nov. is proposed. The type strain of Aquipuribacter hungaricus is IV-75(T) (=DSM 21674(T)=NCAIM B 02333(T)). PMID:21515710

Tóth, E M; Kéki, Zs; Bohus, V; Borsodi, A K; Márialigeti, K; Schumann, P

2012-03-01

366

Marihabitans asiaticum gen. nov., sp. nov., a meso-diaminopimelic acid-containing member of the family Intrasporangiaceae.  

PubMed

Strain HG667(T), isolated from surface seawater collected at the Kesennuma ferry port in Miyagi Prefecture, Japan, was found to be a Gram-positive, catalase-positive bacterium comprising irregular short rods and cocci. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major menaquinone was MK-8(H4). Mycolic acids were not detected. The G+C content of the DNA was 70 mol%. Analysis of the 16S rRNA gene sequence revealed that the strain represents a novel lineage within the family Intrasporangiaceae, order Actinomycetales, being associated with the genus Kribbia. On the basis of morphological, biochemical and chemotaxonomic properties of the strain, together with phylogenetic data relating to the 16S rRNA gene sequence, HG667(T) represents a novel genus and species in the family Intrasporangiaceae, for which the name Marihabitans asiaticum gen. nov., sp. nov. is proposed. The type strain of Marihabitans asiaticum is HG667(T) (=MBIC07497(T) =DSM 18935(T)). PMID:18842869

Kageyama, Akiko; Haga, Tomomi; Kasai, Hiroaki; Shizuri, Yoshikazu; Omura, Satoshi; Takahashi, Yoko

2008-10-01

367

Status of Corynosoma (Acanthocephala: Polymorphidae) based on anatomical, ecological, and phylogenetic evidence, with the erection of Pseudocorynosoma n. gen.  

PubMed

The possession of genital spines has been considered as a key taxonomic trait to differentiate Corynosoma from other genera of the Polymorphidae. However, Corynosoma currently consists of 2 groups of species with clear ecological and morphological divergences: the "marine" group (with ca. 30 species) infects mammals and piscivorous birds in the marine realm, whereas the "freshwater" group (with ca. 7 species) infects waterfowl in continental waters. Species from these groups differ in shape of body and neck, trunk spination, lemnisci length and shape, testes arrangement, and number and shape of cement glands. We tested whether species from these 2 groups formed a monophyletic assemblage based on a phylogenetic analysis by using 15 morphological characters. We also included species of Andracantha, Polymorphus, and Hexaglandula with which potential taxonomic conflicts could most likely arise. We obtained 108 equally most parsimonious trees of 32 steps, with a consistency index (CI) = 0.59, and a retention index (RI) = 0.82. The strict consensus tree indicated that the "freshwater" species of Corynosoma form a monophyletic assemblage closely related to some species of Polymorphus, whereas the "marine" species of Corynosoma are grouped together with Andracantha. Accordingly, Corynosoma is not a monophyletic assemblage, and Pseudocorynosoma n. gen. is proposed for the "freshwater" species of Corynosoma. This decision was strongly supported by (1) a functional comparison of foretrunk muscles between species of Polymophus, Andracantha, and Corynosoma; (2) a multivariate morphometric study of proboscis characters and egg size; and (3) an analysis of ecological patterns of host-parasite relationships. PMID:16883999

Aznar, F Javier; Pérez-Ponce de León, Gerardo; Raga, Juan A

2006-06-01

368

Cerasibacillus quisquiliarum gen. nov., sp. nov., isolated from a semi-continuous decomposing system of kitchen refuse.  

PubMed

A moderately thermophilic and alkaliphilic bacillus, which had been reported and designated BLx (Haruta et al., 2002), was isolated from a semi-continuous decomposing system of kitchen refuse. Cells of strain BLxT were strictly aerobic, rod-shaped, motile and spore forming. The optimum temperature and pH for growth were approximately 50 degrees C and pH 8-9. Strain BLxT was able to grow at NaCl concentrations from 0.5 to 7.5%, with optimum growth at 0.5% NaCl. The predominant menaquinone was MK-7, and the major fatty acid was iso-C(15 : 0). Phylogenetic analysis showed that strain BLxT was positioned in an independent lineage within the cluster that includes the genera Virgibacillus and Lentibacillus in Bacillus rRNA group 1. Strain BLxT exhibited 16S rDNA similarity of 92.8-94.8% to Virgibacillus species and 92.3% to Lentibacillus salicampi. Phenotypic, chemotaxonomic and phylogenetic analyses supported the classification of strain BLxT in a novel genus and species. Cerasibacillus quisquiliarum gen. nov., sp. nov. is proposed on the basis of phenotypic, chemotaxonomic and phylogenetic data. The type strain is BLxT (DSM 15825T=IAM15044T=KCTC 3815T). PMID:15280270

Nakamura, Kohei; Haruta, Shin; Ueno, Shintaro; Ishii, Masaharu; Yokota, Akira; Igarashi, Yasuo

2004-07-01

369

Gelidivirgula Patagoniensis Gen. Nov., Sp. Nov., A Novel Psychrotolerant, Sporeforming Anaerobe Isolated from Magellanic Penguin Guano in Patagonia, Chile  

NASA Technical Reports Server (NTRS)

A novel obligately anaerobic, psychrotrophic bacterium, strain PPP2(sup T), was isolated from guano of the Magellanic penguin (Spheniscus magellanicus) in Patagonia, Chile. The Gram-positive, sporeforming, straight rods with sizes 0.6-0.9 x 3.0-5.0 microns, are motile by peritrichous flagella. Growth was observed to occur within the pH range 6.0-9.5 (optimum pH x), and temperature range 2-28 C (optimum 20 C). The novel isolate does not require NaCl for growth, but is halotolerant and growth was observed between 0 and 7 % NaCl (w/v) with optimum at 0.5 % (w/v). The new isolate is a catalase negative chemoorganohetherotroph with fermentative metabolism and uses as substrates: peptone, Bacto-tryptone, Casamino acids, and yeast extract. The major metabolic products are: acetate, butyrate, ethanol, and hydrogen is a minor gas product.. Strain PPP2 was sensitive to ampicillin, tetracycline, chloramphenicol, rifampin, kanamycin, and gentamycin. The G+C content of the DNA is 43.6 mol%. On the basis of 16S rDNA gene sequences and phenotypic characteristics, it is proposed that the strain PPP2(sup T) (= ATCC BAA-755(sup T) = JSM ...(sup T)) is assigned to the new genus Gelidivirgula gen. nov., as a representative of the new species, Gelidivirgula patagonensis sp. nov.

Pikuta, Elena V.; Hoover, Richard B.; Marsic, Damien; Whitman, William B.; Tang, Jane; Krader, Paul

2003-01-01

370

Roseovarius tolerans gen. nov., sp. nov., a budding bacterium with variable bacteriochlorophyll a production from hypersaline Ekho Lake.  

PubMed

Eight Gram-negative, aerobic, pointed and budding bacteria were isolated from various depths of the hypersaline, heliothermal and meromictic Ekho Lake (Vestfold Hills, East Antarctica). The cells contained storage granules and daughter cells could be motile. Bacteriochlorophyll a was sometimes produced, but production was repressed by constant dim light. The strains tolerated a wide range of temperature, pH, concentrations of artificial seawater and NaCl, but had an absolute requirement for sodium ions. Glutamate was metabolized with and without an additional source of combined nitrogen. The dominant fatty acid was C18:1; other characteristic fatty acids were C18:2, C12:0 2-OH, C12:1 3-OH, C16:1, C16:0 and C18:0. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The DNA G+C base composition was 62-64 mol%. 16S rRNA gene sequence comparisons showed that the isolates were phylogenetically close to the genera Antarctobacter, 'Marinosulfonomonas', Octadecabacter, Sagittula, Sulfitobacter and Roseobacter. Morphological, physiological and genotypic differences to these previously described and distinct genera support the description of a new genus and a new species, Roseovarius tolerans gen. nov., sp. nov. The type strain is EL-172T (= DSM 11457T). PMID:10028255

Labrenz, M; Collins, M D; Lawson, P A; Tindall, B J; Schumann, P; Hirsch, P

1999-01-01

371

Rubidimonas crustatorum gen. nov., sp. nov., a novel member of the family Saprospiraceae isolated from a marine crustacean.  

PubMed

A strictly aerobic, Gram-negative, reddish-orange pigmented, non-motile and rod-shaped bacterium, designated AK17-053(T) was isolated from a marine crustacean (Squillidae) living on tidal flats on the coast of the Ariake Sea, Nagasaki, Japan. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the novel isolate could be affiliated with the family Saprospiraceae of the phylum Bacteroidetes and that it showed highest sequence similarity (84%) with Lewinella marina MKG-38(T). The strain could be differentiated phenotypically from recognized members of the family Saprospiraceae. The G+C content of DNA was 55.3 mol%, MK-7 was the major menaquinone and iso-C(15:0) and C(16:1)?7c were the major fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that strain AK17-053(T) represents a new genus of the family Saprospiraceae. We propose the name Rubidimonas crustatorum gen. nov., sp. nov. for this strain; its type strain is AK17-053(T) (= MBIC08356(T) = NBRC 107717(T)). PMID:21993690

Yoon, Jaewoo; Katsuta, Atsuko; Kasai, Hiroaki

2012-03-01

372

Spongitalea numazuensis gen. nov., sp. nov., a new marine bacterium of the family Flavobacteriaceae isolated from an unidentified marine sponge.  

PubMed

Polyphasic taxonomic investigation was conducted on a strictly aerobic, Gram-negative, non-motile, pale-yellow-pigmented, rod-shaped strain designated HJ24(T) which was isolated from an unidentified orange-colored marine sponge. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the novel isolate could be affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (88.6%) with Pseudozobellia thermophila KMM 3531(T). The novel isolate is phenotypically and physiologically different from other related genera. The DNA G+C contents were 41 mol%, MK-6 was the major menaquinone and iso-C15:0, iso-C15:1 and iso-C17:0 3-OH were the predominant fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that the novel strain represents a new genus and a novel species of the family Flavobacteriaceae. We propose the name Spongitalea numazuensis gen. nov., sp. nov. for this strain; its type strain is HJ24(T) (= DSM 21243(T)). PMID:23149683

Mitra, Sharbanee; Nishijima, Miyuki; Kasai, Hiroaki; Yokota, Akira; Yoon, Jaewoo

2012-01-01

373

Factors Influencing the Decisions and Actions of Pilots and Air Traffic Controllers in Three Plausible NextGen Environments  

NASA Technical Reports Server (NTRS)

In the current air traffic management (ATM) system, pilots and air traffic controllers have well-established roles and responsibilities: pilots fly aircraft and are concerned with energy management, fuel efficiency, and passenger comfort; controllers separate aircraft and are concerned with safety and management of traffic flows. Despite having different goals and obligations, both groups must be able to effectively communicate and interact with each other for the ATM system to work. This interaction will become even more challenging as traffic volume increases dramatically in the near future. To accommodate this increase, by 2025 the national air transportation system in the U.S. will go through a transformation that will modernize the ATM system and make it safer, more effective, and more efficient. This new system, NextGen, will change how pilots and controllers perform their tasks by incorporating advanced technologies and employing new procedures. It will also distribute responsibility between pilots, controllers and automation over such tasks as maintaining aircraft separation. The present chapter describes three plausible concepts of operations that allocate different ATM responsibilities to these groups. We describe how each concept changes the role of each operator and the types of decisions and actions performed by them.

Vu, Kim-Phuong L.; Strybel, Thomas Z.; Battiste, Vernol; Johnson, Walter

2011-01-01

374

Desulfatiferula olefinivorans gen. nov., sp. nov., a long-chain n-alkene-degrading, sulfate-reducing bacterium.  

PubMed

A novel anaerobic, long-chain alkene-degrading, sulfate-reducing bacterium, strain LM2801T, was isolated from brackish sediment of a wastewater decantation facility of an oil refinery (Berre lagoon, France). Cells of strain LM2801T were Gram-negative, motile, slightly curved or vibrioid rods. Its optimum growth conditions were 30-36 degrees C, 6-10 g NaCl l(-1) and pH 7.5. Strain LM2801T incompletely oxidized long-chain alkenes (from C14 to C23) and fatty acids (C14 to C24). The DNA G+C content was 45.5 mol%. Sequence analyses of the 16S rRNA and dsrAB genes indicated that the strain was a member of the family Desulfobacteraceae within the Deltaproteobacteria. This novel isolate possesses phenotypic and phylogenetic traits that do not allow its classification as a member of any previously described genus. Therefore, strain LM2801T is described as a member of a new genus, Desulfatiferula gen. nov., of which Desulfatiferula olefinivorans sp. nov. is the type species. The type strain of Desulfatiferula olefinivorans is LM2801T (=DSM 18843T=JCM 14469T). PMID:17978243

Cravo-Laureau, Cristiana; Labat, Cindy; Joulian, Catherine; Matheron, Robert; Hirschler-Réa, Agnès

2007-11-01

375

Desulfatibacillum aliphaticivorans gen. nov., sp. nov., an n-alkane- and n-alkene-degrading, sulfate-reducing bacterium.  

PubMed

A novel marine sulfate-reducing bacterium, strain CV2803T, which is able to oxidize aliphatic hydrocarbons, was isolated from a hydrocarbon-polluted marine sediment (Gulf of Fos, France). The cells were rod-shaped and slightly curved, measuring 0.6x2.2-5.5 microm. Strain CV2803T stained Gram-negative and was non-motile and non-spore-forming. Optimum growth occurred in the presence of 24 g NaCl l(-1), at pH 7.5 and at a temperature between 28 and 35 degrees C. Strain CV2803T oxidized alkanes (from C13 to C18) and alkenes (from C7 to C23). The DNA G+C content was 41.4 mol%. Comparative sequence analyses of the 16S rRNA gene and dissimilatory sulfite reductase (dsrAB) gene and those of other sulfate-reducing bacteria, together with its phenotypic properties, indicated that strain CV2803T was a member of a distinct cluster that contained unnamed species. Therefore, strain CV2803T (=DSM 15576T=ATCC BAA-743T) is proposed as the type strain of a novel species in a new genus, Desulfatibacillum aliphaticivorans gen. nov., sp. nov. PMID:14742462

Cravo-Laureau, Cristiana; Matheron, Robert; Cayol, Jean-Luc; Joulian, Catherine; Hirschler-Réa, Agnès

2004-01-01

376

Planifilum fimeticola gen. nov., sp. nov. and Planifilum fulgidum sp. nov., novel members of the family 'Thermoactinomycetaceae' isolated from compost.  

PubMed

Four thermophilic, Gram-positive strains, designated H0165(T), 500275(T), C0170 and 700375, were isolated from a composting process in Japan. The isolates grew aerobically at about 65 degrees C on a solid medium with formation of substrate mycelia; spores were produced singly along the mycelia. These morphological characters resembled those of some type strains of species belonging to the family 'Thermoactinomycetaceae', except that aerial mycelia were not formed. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the closest related species to the isolates were members of the family 'Thermoactinomycetaceae', but that the isolates formed an independent phylogenetic lineage. Some chemotaxonomic characters of the isolates, such as DNA G+C contents of 58.7-60.3 mol%, MK-7 as the major menaquinone and cellular fatty acid profiles, differed from those of members of the family 'Thermoactinomycetaceae'. DNA-DNA hybridization showed that the isolates could be divided into two genomic groups, strain H0165(T) and the other three strains. These results indicated that the four isolates should be classified into two species of a novel genus in the family 'Thermoactinomycetaceae', for which the names Planifilum fimeticola gen. nov., sp. nov. (type strain H0165(T)=ATCC BAA-969(T)=JCM 12507(T)) and Planifilum fulgidum sp. nov. (type strain 500275(T)=ATCC BAA-970(T)=JCM 12508(T)) are proposed. PMID:16166716

Hatayama, Kouta; Shoun, Hirofumi; Ueda, Yasuichi; Nakamura, Akira

2005-09-01

377

Nicoletella semolina gen. nov., sp. nov., a New Member of Pasteurellaceae Isolated from Horses with Airway Disease  

PubMed Central

Gram-negative, nonmotile bacteria that are catalase, oxidase, and urease positive are regularly isolated from the airways of horses with clinical signs of respiratory disease. On the basis of the findings by a polyphasic approach, we propose that these strains be classified as Nicoletella semolina gen. nov, sp. nov., a new member of the family Pasteurellaceae. N. semolina reduces nitrate to nitrite but is otherwise biochemically inert; this includes the lack of an ability to ferment glucose and other sugars. Growth is fastidious, and the isolates have a distinctive colony morphology, with the colonies being dry and waxy and looking like a semolina particle that can be moved around on an agar plate without losing their shape. DNA-DNA hybridization data and multilocus phylogenetic analysis, including 16S rRNA gene (rDNA), rpoB, and infB sequencing, clearly placed N. semolina as a new genus in the family Pasteurellaceae. In all the phylogenetic trees constructed, N. semolina is on a distinct branch displaying ?5% 16S rDNA, ?16% rpoB, and ?20% infB sequence divergence from its nearest relative within the family Pasteurellaceae. High degrees of conservation of the 16S rDNA (99.8%), rpoB (99.6%), and infB (99.7%) sequences exist within the species, indicating that N. semolina isolates not only are phenotypically homogeneous but also are genetically homogeneous. The type strain of N. semolina is CCUG43639T (DSM16380T).

Kuhnert, Peter; Korczak, Bozena; Falsen, Enevold; Straub, Reto; Hoops, Anneliese; Boerlin, Patrick; Frey, Joachim; Mutters, Reinier

2004-01-01

378

GenHtr: a tool for comparative assessment of genetic heterogeneity in microbial genomes generated by massive short-read sequencing  

PubMed Central

Background Microevolution is the study of short-term changes of alleles within a population and their effects on the phenotype of organisms. The result of the below-species-level evolution is heterogeneity, where populations consist of subpopulations with a large number of structural variations. Heterogeneity analysis is thus essential to our understanding of how selective and neutral forces shape bacterial populations over a short period of time. The Solexa Genome Analyzer, a next-generation sequencing platform, allows millions of short sequencing reads to be obtained with great accuracy, allowing for the ability to study the dynamics of the bacterial population at the whole genome level. The tool referred to as GenHtr was developed for genome-wide heterogeneity analysis. Results For particular bacterial strains, GenHtr relies on a set of Solexa short reads on given bacteria pathogens and their isogenic reference genome to identify heterogeneity sites, the chromosomal positions with multiple variants of genes in the bacterial population, and variations that occur in large gene families. GenHtr accomplishes this by building and comparatively analyzing genome-wide heterogeneity genotypes for both the newly sequenced genomes (using massive short-read sequencing) and their isogenic reference (using simulated data). As proof of the concept, this approach was applied to SRX007711, the Solexa sequencing data for a newly sequenced Staphylococcus aureus subsp. USA300 cell line, and demonstrated that it could predict such multiple variants. They include multiple variants of genes critical in pathogenesis, e.g. genes encoding a LysR family transcriptional regulator, 23 S ribosomal RNA, and DNA mismatch repair protein MutS. The heterogeneity results in non-synonymous and nonsense mutations, leading to truncated proteins for both LysR and MutS. Conclusion GenHtr was developed for genome-wide heterogeneity analysis. Although it is much more time-consuming when compared to Maq, a popular tool for SNP analysis, GenHtr is able to predict potential multiple variants that pre-exist in the bacterial population as well as SNPs that occur in the highly duplicated gene families. It is expected that, with the proper experimental design, this analysis can improve our understanding of the molecular mechanism underlying the dynamics and the evolution of drug-resistant bacterial pathogens.

2010-01-01

379

Leifsonia poae gen. nov., sp. nov., isolated from nematode galls on Poa annua, and reclassification of 'Corynebacterium aquaticum' Leifson 1962 as Leifsonia aquatica (ex Leifson 1962) gen. nov., nom. rev., comb. nov. and Clavibacter xyli Davis et al. 1984 with two subspecies as Leifsonia xyli (Davis et al. 1984) gen. nov., comb. nov.  

PubMed

The new genus Leifsonia gen. nov. with two new species, Leifsonia poae sp. nov. (type strain VKM Ac-1401T) and Leifsonia aquatica (ex Leifson 1962) nom. rev., comb. nov. (the type species, with VKM Ac-1400T = DSM 20146T = JCM 1368T as type strain), is proposed to accommodate bacteria found in Poa annua root gall, induced by the nematode Subanguina radicicola, and 'Corynebacterium aquaticum' Leifson 1962. Further, it is proposed to reclassify Clavibacter xyli Davis et al. 1984 with two subspecies in the new genus as Leifsonia xyli (Davis et al. 1984) comb. nov., Leifsonia xyli subsp. xyli (Davis et al. 1984) comb. nov. and Leifsonia xyli subsp. cynodontis (Davis et al. 1984) comb. nov. Members of the proposed genus are characterized by coryneform morphology, peptidoglycans based upon 2,4-diaminobutyric acid, the major menaquinone MK-11, phosphatidylglycerol and diphosphatidylglycerol as principal phospholipids, the high content of anteiso- and iso-branched saturated fatty acids, and a DNA G+C base composition of 66-73 mol%. They form a distinct phylogenetic branch attached to the line of descent of Agromyces spp. The new and reclassified species of the new genus clearly differ from each other phylogenetically and phenetically and can be recognized by their morphologies, the cell wall sugar composition, the requirement of complex media for growth, and numerous physiological characteristics, including the oxidase reaction. PMID:10826825

Evtushenko, L I; Dorofeeva, L V; Subbotin, S A; Cole, J R; Tiedje, J M

2000-01-01

380

Genetic relationships among avian isolates classified as Pasteurella haemolytica, 'Actinobacillus salpingitidis' or Pasteurella anatis with proposal of Gallibacterium anatis gen. nov., comb. nov. and description of additional genomospecies within Gallibacterium gen. nov.  

PubMed

Bacteria of the avian [Pasteurella haemolytica]-'Actinobacillus salpingitidis' complex have been associated with different pathological conditions in birds, among which salpingitis and peritonitis in chickens of layer type seem to dominate. The aim of this study was to classify these bacteria by comparison of 37 strains tentatively classified as biovars of the avian [P. haemolytica]-'A. salpingitidis' complex or as Pasteurella anatis. PFGE, AFLP and plasmid profiling showed that strains representing different biovars were genotypically different. Phylogenetic analysis of 22 strains characterized by 16S rRNA gene sequence comparison showed that strains classified as biovars 5, 8 and 9 were closely related to the suggested type strain of 'A. salpingitidis' (98.4-99.9% similarity), whereas the remaining strains classified in 12 biovars or as P. anatis were closely related to the type strain of P. anatis (98.1-100% similarity). The two groups were related at 95.7-97.1% similarity. The closest similarity outside this group was 94.6%, between biovar 15 and Bisgaard taxon 3. DNA-DNA hybridization was performed with 34 strains and showed binding above 85% for strains of biovars 5 and 8, including the suggested type strain of 'A. salpingitidis'. Two strains of P. anatis (F 149T and F 279) were closely related at 79% DNA binding to 27 strains of biovars 1,3, 4, 11, 12, 17-20, 22 and 24. A new genus, Gallibacterium gen. nov., is proposed to include the avian [P. haemolytica]-'A. salpingitidis'-P. anatis complex, since these taxa form a monophyletic unit with similarities above 95% on the basis of 16S rRNA sequence comparison and they are unrelated to other genera of the family Pasteurellaceae Pohl 1981. The new genus consists of Gram-negative, non-motile, rod-shaped or pleomorphic bacteria. The bacteria are catalase-, oxidase- and phosphatase-positive. Nitrate is reduced and acid is produced without gas formation from glycerol, (-)D-ribose, (+)D-xylose, (-)D-mannitol, (-)D-fructose, (+)D-galactose, (+)D-glucose, (+)D-mannose, sucrose and raffinose. The genus Gallibacterium can be separated from other genera of Pasteurellaceae by differences in catalass, symbiotic growth, haemolysis, urease, indole, acid production from (+)D-xylose, (-)D-mannitol, (-)D-sorbitol, (+)D-mannose, maltose, raffinose and dextrin and ONPG and PNPG tests. Pasteurella anatis Mutters et al. 1985 is transferred to the new genus as Gallibacterium anatis gen. nov., comb. nov. Genomospecies 1 of Gallibacterium is proposed to include the former biovars 5 and 8 of the avian [P. haemolytica]-'A. salpingitidis' complex. The type strain of Gallibacterium anatis is F 149T (=ATCC 43329T = NCTC 11413T) and the reference strain of Gallibacterium genomospecies 1 is CCM 5974. PMID:12656185

Christensen, Henrik; Bisgaard, Magne; Bojesen, Anders Miki; Mutters, Reinier; Olsen, John Elmerdahl

2003-01-01

381

Melghirimyces algeriensis gen. nov., sp. nov., a member of the family Thermoactinomycetaceae, isolated from a salt lake.  

PubMed

A novel filamentous bacterium, designated NariEX(T), was isolated from soil collected from Chott Melghir salt lake, which is located in the south-east of Algeria. The strain was an aerobic, halotolerant, thermotolerant, Gram-positive bacterium that was able to grow in NaCl concentrations up to 21% (w/v), at 37-60 °C and at pH 5.0-9.5. The major fatty acids were iso- and anteiso-C(15:0). The DNA G+C content was 47.3 mol%. The major menaquinone was MK-7, but MK-6 and MK-8 were also present. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine (methyl-PE). Results of molecular and phenotypic analysis led to the description of the strain as a new member of the family Thermoactinomycetaceae. The isolate was distinct from members of recognized genera of this family by morphological, biochemical and chemotaxonomic characteristics. Strain NariEX(T) showed 16S rRNA gene sequence similarities of 95.38 and 94.28% with the type strains of Desmospora activa and Kroppenstedtia eburnea, respectively, but differed from both type strains in its sugars, polar lipids and in the presence of methyl-PE. On the basis of physiological and phylogenetic data, strain NariEX(T) represents a novel species of a new genus of the family Thermoactinomycetaceae for which the name Melghirimyces algeriensis gen. nov., sp. nov. is proposed. The type strain of Melghirimyces algeriensis, the type species of the genus, is NariEX(T) (=DSM 45474(T)=CCUG 59620(T)). PMID:21856989

Addou, Ammara Nariman; Schumann, Peter; Spröer, Cathrin; Hacene, Hocine; Cayol, Jean-Luc; Fardeau, Marie-Laure

2012-07-01

382

Halomicroarcula pellucida gen. nov., sp. nov., a non-pigmented, transparent-colony-forming, halophilic archaeon isolated from solar salt.  

PubMed

A novel halophilic strain, BNERC31(T), was isolated from solar salt, 'Sel marin de Guérande', imported from France. Colonies on agar medium containing soluble starch, sodium citrate, sodium glutamate and inorganic salts were non-pigmented and transparent, while cells obtained by centrifuging liquid cultures were red-pigmented. Cells of strain BNERC31(T) were non-motile, pleomorphic, stained Gram-negative and lysed in distilled water. Growth occurred with 20-30?% (w/v) NaCl (optimum, 25?%, w/v), with 0-500 mM MgCl2 (optimum, 10 mM), at pH 6.0-8.5 (optimum, pH 7.0) and at 25-55 °C (optimum, 40 °C). Growth was dependent on soluble starch, and inhibited completely by 0.5?% organic nutrients, such as Casamino acids or yeast extract. The DNA G+C content was 64.1 mol%. Strain BNERC31(T) possessed at least two heterogeneous 16S rRNA genes, and the sequence of the orthologous gene (preceded by the dihydroorotate oxidase gene, pyrD) showed the highest similarity (96.5?%) to that of Haloarcula marismortui JCM 8966(T). The RNA polymerase subunit B' gene sequence showed the highest similarity (91.7?%) to that of Haloarcula amylolytica JCM 13557(T). The polar lipids of strain BNERC31(T) were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, diglycosyl diether and sulfated diglycosyl diether, similar to those of species of the genus Halomicrobium. The phenotypic and phylogenetic characteristics showed that strain BNERC31(T) differed from species of the genera Haloarcula and Halomicrobium and indicated that it represents a novel species in a new genus, for which the name Halomicroarcula pellucida gen. nov., sp. nov. is proposed. The type strain of the type species is BNERC31(T) (?=?JCM 17820(T)?=?CECT 7537(T)). PMID:23563231

Echigo, Akinobu; Minegishi, Hiroaki; Shimane, Yasuhiro; Kamekura, Masahiro; Itoh, Takashi; Usami, Ron

2013-10-01

383

Desulfocurvus vexinensis gen. nov., sp. nov., a sulfate-reducing bacterium isolated from a deep subsurface aquifer.  

PubMed

A novel anaerobic, chemo-organotrophic bacterium, designated VNs36(T), was isolated from a well that collected water from a deep saline aquifer used for underground gas storage at a depth of 830 m in the Paris Basin, France. Cells were curved motile rods or vibrios (3.0-5.0x0.5 microm). Strain VNs36(T) grew at temperatures between 20 and 50 degrees C (optimum 37 degrees C) and at pH values between 5.0 and 9.0 (optimum 6.9). It did not require salt for growth, but tolerated up to 20 g NaCl l(-1) (optimum 2 g l(-1)). In the presence of sulfate, strain VNs36(T) used lactate, formate and pyruvate as carbon and energy sources. The main fermentation products from lactate were acetate, H(2) and CO(2). Sulfate, thiosulfate and sulfite were used as electron acceptors, but not sulfur. The genomic DNA G+C content of strain VNs36(T) was 67.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain VNs36(T) was affiliated with the family Desulfovibrionaceae within the class Deltaproteobacteria. On the basis of 16S rRNA gene sequence comparisons, DNA G+C content and the absence of desulfoviridin in cell extracts, it is proposed that strain VNs36(T) be assigned to a new genus, Desulfocurvus gen. nov., as a representative of a novel species, Desulfocurvus vexinensis sp. nov. The type species of this genus is Desulfocurvus vexinensis with the type strain VNs36(T) (=DSM 17965(T)=JCM 14038(T)). PMID:19643880

Klouche, Nihel; Basso, Odile; Lascourrèges, Jean-François; Cayol, Jean-Luc; Thomas, Pierre; Fauque, Guy; Fardeau, Marie-Laure; Magot, Michel

2009-12-01

384

Rubidibacter lacunae gen. nov., sp. nov., a unicellular, phycoerythrin-containing cyanobacterium isolated from seawater of Chuuk lagoon, Micronesia.  

PubMed

A unicellular cyanobacterium, designated KORDI 51-2(T), was isolated from surface seawater of Chuuk lagoon, Micronesia. The cells were wine-coloured rods and emitted red fluorescence under green excitation of an epifluorescence microscope. Thus, morphologically, the strain resembled Synechococcus species. However, based on 16S rRNA gene sequence similarities between strain KORDI 51-2(T) and related strains belonging to cyanobacteria, the novel strain was distantly related to members of the 'Halothece' cluster. However, sequence similarities between strain KORDI 51-2(T) and members of the 'Halothece' cluster were very low, ranging from 90.7 to 92.1 %, and phylogenetic analyses showed that the strain formed a distinct branch. Therefore, a polyphasic characterization including morphology, physiology and pigment composition was conducted to elucidate the taxonomic position of strain KORDI 51-2(T). The strain grew within a temperature range of 25-35 degrees C and a salinity range of 2-7 %. The optimal temperature and salinity were about 30 degrees C and 5 %, respectively. Strain KORDI 51-2(T) contained phycoerythrin, and the dominant carotenoid pigments were zeaxanthin, beta-carotene and echinenone. The DNA G+C content was 60.5 mol%. Based on phylogenetic analysis of the 16S rRNA gene sequence, and the physiological data and pigment compositions, strain KORDI 51-2(T) is considered to represent a new genus and novel species of cyanobacteria for which the name Rubidibacter lacunae gen. nov., sp. nov. is proposed. The type strain is KORDI 51-2(T) (=KCTC 40015(T)=UTEX L2944(T)). PMID:19060063

Choi, Dong Han; Noh, Jae Hoon; Lee, Charity M; Rho, Seungmok

2008-12-01

385

Comparative morphology and molecular phylogeny of Apicoporus n. Gen.: a new genus of marine benthic dinoflagellates formerly classified within Amphidinium.  

PubMed

The composition of the dinoflagellate genus Amphidinium is currently polyphyletic and includes several species in need of re-evaluation using modern morphological and phylogenetic methods. We investigated a broad range of uncultured morphotypes extracted from marine sediments in the Eastern Pacific Ocean that were similar in morphology to Amphidinium glabrum Hoppenrath and Okolodkov. To determine the number of distinct species associated with this phenotypic diversity, we collected LM, SEM, TEM and small subunit ribosomal DNA sequence information from different morphotypes, including the previously described A. glabrum. Both comparative morphological and molecular phylogenetic data supported the establishment of a new genus, Apicoporus n. gen., including at least two species, A. glaber n. comb., and A. parvidiaboli n. sp. Apicoporus is characterized by having amphiesmal pores and an apical pore covered by a hook-like protrusion; neither of these characters has been observed in other athecate dinoflagellates. The posterior end of Apicoporus parvidiaboli possessed varying degrees of "horn formation", ranging from slight to prominent. By contrast, the posterior end of Apicoporus glaber was distinctively rounded and lacked evidence of horn formation. Although these species were previously interpreted to be obligate heterotrophs, TEM and epifluorescence microscopy demonstrated that some cells of both species had unusually small but otherwise typical dinoflagellate plastids. The number and density of plastids in any particular cell varied significantly in the genus, but the plastids were almost always concentrated at the posterior end of the cells or around the nucleus. The presence of cryptic photosynthetic plastids in these benthic species suggests that photosynthesis might be much more widespread in dinoflagellates than is currently assumed. PMID:18325833

Sparmann, Sarah F; Leander, Brian S; Hoppenrath, Mona

2008-07-01

386

Jeotgalibaca dankookensis gen. nov., sp. nov., a member of the family Carnobacteriaceae, isolated from seujeot (Korean traditional food).  

PubMed

A novel, Gram-stain-positive bacterium, designated strain EX-07(T), was isolated from seujeot (Korean traditional food). The strain was aerobic, halotolerant and non-motile; it formed cocci that grouped into tetrads and sarcinae or formed irregular conglomerates. Growth occurred at pH 7-9, at 10-37 °C and with up to 9?% NaCl. Isolate EX-07(T) was catalase- and oxidase-negative and used sugars and organic acids as carbon sources. The 16S rRNA gene sequence of the novel strain showed 94.2-94.5?% similarity with the type strains of Trichococcus pasteurii, Trichococcus patagoniensis, Trichococcus collinsii, Trichococcus flocculiformis and Trichococcus palustris and only 92.2?% with representatives of the genera Bavariicoccus, Carnobacterium and Granulicatella. Sequence similarities based on the groEL gene ranged from 81.3 to 82.8?% between the novel isolate and the type strains of all species of the genus Trichococcus, and only 74.2 and 75.3?% with type strains of members of the genera Bavariicoccus and Granulicatella, respectively. The G+C content of the genomic DNA was 39.6 mol%. The predominant fatty acids were C16?:?1?9c, C18?:?1?9c, C16?:?0 and C14?:?0. The polar lipid profile was very complex and included phosphatidylethanolamine and several unidentified aminolipids, glycolipids and phospholipids. Based on the genotypic and phenotypic results obtained in this study, it is proposed that isolate EX-07(T) represents a novel species of a new genus in the family Carnobacteriaceae for which the name Jeotgalibaca dankookensis gen. nov., sp. nov. is proposed. The type strain of Jeotgalibaca dankookensis is EX-07(T) (?=?KCCM 90229(T)?=?JCM 19215(T)). PMID:24554638

Lee, Dong-Geol; Trujillo, Martha E; Kang, Heecheol; Ahn, Tae-Young

2014-05-01

387

Blastocatella fastidiosa gen. nov., sp. nov., isolated from semiarid savanna soil - the first described species of Acidobacteria subdivision 4.  

PubMed

Acidobacteria represent abundant members of soil microbial communities but only few representatives could be isolated and validly described so far. Currently, eighteen species of subdivision 1, one species of subdivision 3, three species of subdivision 8, and one species of subdivision 10 are recognized. In contrast, Acidobacteria of subdivision 4 have largely escaped cultivation although they belong to the most abundant and diverse acidobacterial groups in soils. A member of subdivision 4, strain A2-16(T), was isolated from a semiarid savanna soil. Cells were motile spheres to rods with a tendency to form chains and larger aggregates. Cultures were orange to pink colored, neutrophilic mesophiles, and showed aerobic chemoorganoheterotrophic growth on very few complex substrates and protocatechuate, and weak growth on chitin, cellulose and starch. While protein substrates such as casamino acids or peptone were utilized, individual amino acids did not promote growth. Also, growth on alternative electron acceptors or fermentative growth could not be observed. Major fatty acids were summed features 1 (15:1 iso H/13:0 3-OH) and 3 (16:1?7c/15:0 iso 2-OH). The major quinone was MK-8. The DNA G+C content was 46.5mol%. Phylogenetic analysis placed A2-16(T) amidst uncultured members of Acidobacteria subdivision 4. The most closely related environmental 16S rRNA gene sequences (96-97% nucleotide identity) were several clone sequences from terrestrial environments. Based on these characteristics, the isolated strain is proposed as a new species of a novel genus, Blastocatella fastidiosa gen. nov., sp. nov. The type strain of B. fastidiosa is A2-16(T) (=DSM 25172(T)=LMG26944(T)). PMID:23266188

Foesel, Bärbel U; Rohde, Manfred; Overmann, Jörg

2013-03-01

388

Alpinimonas psychrophila gen. nov., sp. nov., an actinobacterium of the family Microbacteriaceae isolated from alpine glacier cryoconite.  

PubMed

A Gram-type positive, Gram-reaction variable, non-motile, psychrophilic actinobacterium, designated Cr8-25(T), was isolated from alpine glacier cryoconite and was able to grow well over a temperature range of 1-15 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Cr8-25(T) belonged to the family Microbacteriaceae and showed highest 16S rRNA gene sequence similarity with Klugiella xanthotipulae 44C3(T) (97.0%). However, strain Cr8-25(T) could be differentiated from the type strain of K. xanthotipulae on the level of genomospecies by a DNA-DNA relatedness value of only 37.2%. Strain Cr8-25(T) contained a cell-wall peptidoglycan that was cross-linked according to the B-type, which is based on 2,4-diaminobutyric acid. The cell wall contained the sugars galactose, fucose and rhamnose. The predominant cellular fatty acids of strain Cr8-25(T) were C(15:0) anteiso (64.6%) and iso-C(16:0) (22.5%) and the major menaquinones were MK-11 and MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and unknown glycolipids. The G+C content of the genomic DNA was 58.8 mol%. On the basis of the phenotypic characteristics, phylogenetic and chemotaxonomic analyses and DNA-DNA relatedness data, strain Cr8-25(T) represents a novel species of a new genus in the family Microbacteriaceae, for which the name Alpinimonas psychrophila gen. nov., sp. nov. is proposed. The type strain is Cr8-25(T) (=DSM 23737(T)=LMG 26215(T)). PMID:22228665

Schumann, Peter; Zhang, De-Chao; Redzic, Mersiha; Margesin, Rosa

2012-11-01

389

Glaciimonas immobilis gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from alpine glacier cryoconite.  

PubMed

Strains Cr9-30(T) and Cr9-12 were isolated from alpine glacier cryoconite. Both strains were Gram-negative-staining, non-motile, rod-shaped and psychrophilic, showing good growth over the temperature range 1-20 °C. Phylogenetic analysis of 16S rRNA gene sequences revealed that the two strains formed a distinct branch within the family Oxalobacteraceae and were most closely related to members of the genus Collimonas. The 16S rRNA gene sequence similarity between strains Cr9-30(T) and Cr9-12 was 99.0?%. The two strains showed highest 16S rRNA gene sequence pairwise similarity with Collimonas pratensis LMG 23965(T) (96.6 and 96.1?% for strains Cr9-30(T) and Cr9-12, respectively), Collimonas arenae LMG 23964(T) (96.5 and 96.3?%, respectively) and Collimonas fungivorans LMG 21973(T) (96.4 and 96.2?%, respectively). The predominant cellular fatty acids were summed feature 3 (C??:??7c and/or iso-C??:? 2-OH), C??:? and C??:??7c. The DNA G+C content of strain Cr9-30(T) was 51.0 mol%. On the basis of phenotypic characteristics and phylogenetic analysis, strains Cr9-30(T) and Cr9-12 represent a novel species in a new genus of the family Oxalobacteraceae, for which the name Glaciimonas immobilis gen. nov., sp. nov. is proposed. The type strain of Glaciimonas immobilis is Cr9-30(T) (?=?DSM 23240(T)?=?LMG 25547(T)). PMID:20935085

Zhang, De-Chao; Redzic, Mersiha; Schinner, Franz; Margesin, Rosa

2011-09-01

390

Hoplitolyda duolunica gen. et sp. nov. (Insecta, Hymenoptera, Praesiricidae), the Hitherto Largest Sawfly from the Mesozoic of China  

PubMed Central

Background Large body size of an insect, in general, enhances its capability of predation, competition, and defense, resulting in better survivability and reproduction. Hymenopterans, most being phytophagous or parasitic, have a relatively small to medium body size, typically under 50.0 mm in body length. Principal Findings Herein, we describe Hoplitolyda duolunica gen. et sp. nov., assigned to Praesiricidae, from the Early Cretaceous Yixian Formation of China. This new species is the largest fossil hymenopteran hitherto with body estimated >55.0 mm long and wing span >92.0 mm. H. duolunica is, to our knowledge, the only sawfly with Sc present in the hind wing but not in the forewing. Its Rs1 and M1 meeting each other at 145° angle represents an intermediate in the transition from “Y” to “T” shapes. Even though Hoplitolyda differs significantly from all previously described genera in two subfamilies of Praesricidae, we leave the new genus unplaced in existing subfamilies, pending discovery of material with more taxonomic structure. Conclusions/Significance Hoplitolyda has many unique and interesting characters which might have benefitted its competition, survival, and reproduction: large body size and head with robust and strong mandibles for defense and/or sexual selection, unique wing venation and setal arrangements for flight capability and mobility, dense hairs on body and legs for sensing and protection, etc. Considering the reported ferocious predators of feathered dinosaurs, pterosaurs, birds, and mammals coexisting in the same eco-system, Hoplitolyda is an interesting case of “survival of the fittest” in facing its evolutionary challenges.

Gao, Taiping; Shih, Chungkun; Rasnitsyn, Alexandr P.; Ren, Dong

2013-01-01

391

Zhangella mobilis gen. nov., sp. nov., a new member of the family Hyphomicrobiaceae isolated from coastal seawater.  

PubMed

A Gram-negative, pale-yellow, non-spore-forming bacterium, motile with single polar flagella, strain E6T, was isolated from coastal seawater collected from Tianjin, China, and its taxonomic position was investigated using a polyphasic approach. Strain E6T requires NaCl for growth and grows optimally at pH 8.2 and 36 degrees C and in the presence of 2.0% (w/v) NaCl. It is positive for catalase and oxidase, and reduces nitrate to nitrite. The major fatty acids (>10%) are C18:1omega7c (64.71%) and 11-methyl C18:1omega7c (12.38%), the ubiquinone system is Q-10 and the DNA G+C content is 53.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that strain E6T represented a new lineage in the Alphaproteobacteria and is related to genera Cucumibacter, Devosia, Ochrobactrum and Ahrensia. Strain E6T shows highest 16S rRNA gene sequence similarity (93.3%) to Cucumibacter marinus CL-GR60T and less than 92.2% similarity to other relatives. It can be differentiated from its closest phylogenetic neighbours on the basis of several phenotypic features, including nitrate reduction, assimilation of D-glucose, L-arabinose, D-mannose, mannitol and maltose and major fatty acid composition. A polyphasic analysis supported the conclusion that strain E6T represents a novel genus and species of the family Hyphomicrobiaceae, for which the name Zhangella mobilis gen. nov., sp. nov. is proposed. The type strain of Zhangella mobilis is E6T (=CGMCC 1.7002T=JCM 15144T). PMID:19620375

Xu, Hai-Ying; Chen, Li-Ping; Fu, Song-Zhe; Fan, Hong-Xia; Zhou, Yu-Guang; Liu, Shuang-Jiang; Liu, Zhi-Pei

2009-09-01

392

Desulfovirgula thermocuniculi gen. nov., sp. nov., a thermophilic sulfate-reducer isolated from a geothermal underground mine in Japan.  

PubMed

A thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterial strain, designated RL80JIV(T), was isolated from a geothermally active underground mine in Japan. Cells were rod-shaped and motile. The temperature and pH ranges for growth were 61-80 degrees C (optimum at 69-72 degrees C) and pH 6.4-7.9 (optimum at pH 6.8-7.3), and the strain tolerated up to 0.5 % NaCl. Strain RL80JIV(T) utilized sulfate, sulfite, thiosulfate and elemental sulfur as electron acceptors. Electron donors utilized were H(2) in the presence of CO(2), and carboxylic acids. Fermentative growth occurred on lactate and pyruvate. The cell wall contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was menaquinone MK-7. Major whole-cell fatty acids were iso-C(15 : 0), iso-C(17 : 0) and C(16 : 0). Strain RL80JIV(T) was found to be affiliated with the thiosulfate-reducer Thermanaeromonas toyohensis DSM 14490(T) (90.9 % 16S rRNA gene sequence similarity) and with the sulfate-reducer Desulfotomaculum thermocisternum DSM 10259(T) (90.0 % similarity). Strain RL80JIV(T) is therefore considered to represent a novel species of a new genus, for which the name Desulfovirgula thermocuniculi gen. nov., sp. nov. is proposed. The type strain of Desulfovirgula thermocuniculi is RL80JIV(T) (=DSM 16036(T)=JCM 13928(T)). PMID:17220449

Kaksonen, Anna H; Spring, Stefan; Schumann, Peter; Kroppenstedt, Reiner M; Puhakka, Jaakko A

2007-01-01

393

Aquimonas voraii gen. nov., sp. nov., a novel gammaproteobacterium isolated from a warm spring of Assam, India.  

PubMed

A bacterial strain designated GPTSA 20(T), which was isolated from a warm spring in Assam, India, was characterized by using a polyphasic approach. The cells were Gram-negative, aerobic rods, which could not utilize or produce acid from most of the carbohydrates tested. The predominant fatty acids were C(15:0) iso (25.04%), C(17:1) iso omega9c (19.28%), C(16:0) iso (17.73%) and C(11:0) iso 3-OH (9.34%). The G+C content was 75 mol%. From 16S rRNA gene sequence analysis (1433 nucleotides, continuous stretch), it was confirmed that strain GPTSA 20(T) belonged to the class 'Gammaproteobacteria'. The closest 16S rRNA gene sequence similarity found (98.2%) was with an uncultured bacterium clone, NB-03 (accession no. AB117707), from an autotrophic nitrifying biofilm. Among culturable bacteria, the closest sequence similarities were with Fulvimonas soli (93.0%), Silanimonas lenta (92.8%), Thermomonas hydrothermalis (92.4%), Frateuria aurantia (91.9%), Rhodanobacter lindaniclasticus (91.9%), Thermomonas haemolytica (91.9%) and Pseudoxanthomonas taiwanensis (91.8%); similarities of less than 91.8% were obtained with other members of the class 'Gammaproteobacteria'. From the biochemical, physiological, chemotaxonomic and phylogenetic analysis, it was clear that strain GPTSA 20(T) was quite different from members of known genera of the class 'Gammaproteobacteria'. Therefore, it is proposed that strain GPTSA 20(T) represents a novel species within a new genus, with the name Aquimonas voraii gen. nov., sp. nov. The type strain is GPTSA 20(T) (=MTCC 6713(T)=JCM 12896(T)). PMID:16014470

Saha, P; Krishnamurthi, S; Mayilraj, S; Prasad, G S; Bora, T C; Chakrabarti, T

2005-07-01

394

Lacticigenium naphtae gen. nov., sp. nov., a halotolerant and motile lactic acid bacterium isolated from crude oil.  

PubMed

A novel lactic acid bacterium, strain MIC1-18(T), was isolated from crude oil collected at an oil-water well in Akita, Japan. Cells of strain MIC1-18(T) were found to be facultatively anaerobic, mesophilic, neutrophilic, Gram-negative, non-sporulating, motile by means of peritrichous flagella and oval rods, 1.8-2.5 mum long. Optimum growth was observed at 30 degrees C, pH 7.0 and 3 % (w/v) NaCl. Strain MIC1-18(T) produced acid from l-arabinose, ribose, glucose, fructose, mannose, N-acetylglucosamine, amygdalin, arbutin, salicin, cellobiose, maltose, sucrose, trehalose, gentiobiose and 5-ketogluconate. l-Lactic acid was the major end product from glucose. The major cellular fatty acid was C(16 : 1)omega7c. The cell-wall murein type was A4alpha containing Lys-Glu. The G+C content of the genomic DNA was 37.8 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that strain MIC1-18(T) was accommodated as a member of the lactic acid bacteria of the low-G+C content Gram-positive bacteria; the closest neighbour of this organism was Atopococcus tabaci CCUG 48253(T), with only 90.0 % sequence similarity. On the basis of the phenotypic features and phylogenetic position, a novel genus and species, Lacticigenium naphtae gen. nov., sp. nov., are proposed for strain MIC1-18(T) (=NBRC 101988(T)=DSM 19658(T)). PMID:19329605

Iino, Takao; Suzuki, Ken-Ichiro; Harayama, Shigeaki

2009-04-01

395